diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 00000000..23442157 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,15 @@ +_site +.sass-cache +.jekyll-cache +.jekyll-metadata +.git +.github +.claude +vendor +node_modules +bower_components +*.xcf +.DS_Store +.idea +.cursor +.siteimprove diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 00000000..fc41c788 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,15 @@ +FROM ruby:3.3-alpine + +RUN apk add --no-cache \ + build-base \ + git \ + && gem install bundler + +WORKDIR /site + +COPY Gemfile Gemfile.lock ./ +RUN bundle install --jobs 4 + +EXPOSE 4000 + +CMD ["bundle", "exec", "jekyll", "serve", "--host", "0.0.0.0"] diff --git a/README.md b/README.md index 9056ce9a..6d6ca1db 100644 --- a/README.md +++ b/README.md @@ -73,6 +73,20 @@ After installing Jekyll, run the following commands to preview the site: You will now be able to access the help pages locally at `http://0.0.0.0:4000` or `localhost:4000` (default configuration). After the website is built for the first time, you should only need to save the file, wait a second or two for it to rebuild automatically (check the terminal window where you ran `jekyll serve`), then refresh the page to see any changes. +#### Development with Docker + +As an alternative, you can use Docker instead of installing Ruby locally. The only prerequisite is [Docker](https://docs.docker.com/get-docker/). A convenience script wraps the Docker Compose setup: + +``` +./run serve # start dev server at http://localhost:4000 (livereload) +./run build # one-shot production build +./run dev # watch + incremental rebuild (no server) +./run stop # stop running containers +./run clean # remove build artifacts and Docker volumes +``` + +`JEKYLL_PORT` and `JEKYLL_ENV` can be set as environment variables. + ### Maintainer Mugdha diff --git a/_config.yml b/_config.yml index b8209bd0..78db7b91 100644 --- a/_config.yml +++ b/_config.yml @@ -35,6 +35,12 @@ plugins: last-modified-at: date-format: '%Y-%m-%dT%H:%M:%S%:z' +exclude: + - Dockerfile + - docker-compose.yml + - run + - vendor + defaults: - scope: path: '' diff --git a/_includes/_blogcontent/2015-07-15-introducing-bumblebee.md b/_includes/_blogcontent/2015-07-15-introducing-bumblebee.md index 3aa351d3..9948d4ab 100644 --- a/_includes/_blogcontent/2015-07-15-introducing-bumblebee.md +++ b/_includes/_blogcontent/2015-07-15-introducing-bumblebee.md @@ -1,5 +1,5 @@ -
+ADS Bumblebee logo
The Astrophysics Data System (ADS) is a tool for finding astronomy and planetary science publications. ADS currently has three different interfaces: * ~~[ADS “Classic”](http://adsabs.harvard.edu/abstract_service.html) -- the one you all know and love,~~ *We're slowly removing Classic servers from use and the redirects will stop working in the near future. Please update your bookmarks to point directly to the [new website](https://ui.adsabs.harvard.edu/) (edited 11/2021).* diff --git a/_includes/_blogcontent/2015-10-21-visualising-metrics-with-bbb.md b/_includes/_blogcontent/2015-10-21-visualising-metrics-with-bbb.md index cf3bffc2..681bb634 100644 --- a/_includes/_blogcontent/2015-10-21-visualising-metrics-with-bbb.md +++ b/_includes/_blogcontent/2015-10-21-visualising-metrics-with-bbb.md @@ -7,25 +7,25 @@ For many scientists, it's all about the numbers and when it comes to evaluating To get started, go to [ADS Bumblebee](https://ui.adsabs.harvard.edu) and perform an [author query](../help/search/search-syntax/):
- + Screenshot of the ADS Bumblebee author search query form
On the search results page, click the Explore button and select Citation Metrics:
- + Screenshot of the ADS search results page with the Explore menu showing Citation Metrics option
The top panel displayed is a graphical representation of the search results as a histogram of the number of products published per year. - +Histogram showing number of publications per year for a given author in ADS Citation Metrics Use this panel as a sanity check that your search is selecting the publications you are interested in, since all of the indices are calculated based on this set. On the left side of the panel, the total number of publications and the number of those which are refereed are listed. On the histogram, you can mouse over any data point to see the actual values. The first result set is for the default amount of publications (300). If you have more, you can specify that number in the box at the top of the overview (up to the maximum of 2,000). We expect to be able to increase this maximum at some point in the future. There are panels that display information about Citations and Reads, but let’s focus on the Indices. The panel illustrates the values of various indices on any given year. - +Panel showing citation indices including h-index and other metrics over time in ADS On the left, the present value of many popular indices are calculated. Mouse over the help icon next to each index to get a brief description of how it’s calculated. diff --git a/_includes/_blogcontent/2015-11-03-ads-private-libraries.md b/_includes/_blogcontent/2015-11-03-ads-private-libraries.md index 20b68ea7..9514ac96 100644 --- a/_includes/_blogcontent/2015-11-03-ads-private-libraries.md +++ b/_includes/_blogcontent/2015-11-03-ads-private-libraries.md @@ -6,13 +6,13 @@ The ADS libraries allow you to maintain a collection of bibcodes within your own To get started, simply [create an ADS user account](https://ui.adsabs.harvard.edu/#user/account/register) and [make a query](https://ui.adsabs.harvard.edu/#search/q=author%3A"Accomazzi%2C+A.") of the papers you wish to add to a library. Select the papers that you are interested in and you will now have the option to add them to a new library or one that already exists.
- + Screenshot of ADS search results page showing the option to add selected papers to a library

Find your libraries by going to your user area.
- + Screenshot of the ADS user area showing the personal libraries section
You can view metrics, create exports, and visualise graphs for each of your libraries, much like in the standard search result pages. Currently, you can make your libraries public to be viewed by other people with a unique URL by visiting the permissions section. diff --git a/_includes/_blogcontent/2015-11-17-discovering-long-fuse-papers.md b/_includes/_blogcontent/2015-11-17-discovering-long-fuse-papers.md index 5cc8f4c8..168dc599 100644 --- a/_includes/_blogcontent/2015-11-17-discovering-long-fuse-papers.md +++ b/_includes/_blogcontent/2015-11-17-discovering-long-fuse-papers.md @@ -2,7 +2,7 @@ On average, articles get cited in a pretty predictable pattern. An article gets published, it takes a little while to get "absorbed" by the scientific community, and then, if it resonates, it starts getting citations. Something along the lines of figure 4 in my paper "Effect of E-printing on Citation Rates in Astronomy and Physics", Journal of Electronic Publishing, vol. 9, p. 2:
- + Line chart showing the typical citation rate pattern for a paper over time, peaking then declining
In the pre-Internet days, this meant that people had to work their way through abstract books and reading the tables of contents from volumes on the shelves of their local library. The principle, nevertheless, is the same, just with a different time scale. When you have to physically work your way through shelves and volumes, it obviously takes more time to gather your bibliography, when writing a paper in this pre-Internet era. Even when you allow for these longer time scales, there are still papers that take longer, way longer, to be cited than others. Todd Lauer coined the phrase "long-fuse" papers on Twitter (in a discussion with Joss Bland-Hawthorn) and wondered about how to detect these. That is what this blog is about. One attempt at finding them. The figure below shows one fine example of such a "long-fuse" publication: "On the Masses of Nebulae and of Clusters of Nebulae", by F. Zwicky (1937), Astrophysical Journal, vol. 86, p.217 diff --git a/_includes/_blogcontent/2016-02-17-building-an-app.md b/_includes/_blogcontent/2016-02-17-building-an-app.md index 9742745e..76fa3b91 100644 --- a/_includes/_blogcontent/2016-02-17-building-an-app.md +++ b/_includes/_blogcontent/2016-02-17-building-an-app.md @@ -3,22 +3,22 @@ Underneath the new user interface of the ADS, ADS Beta (or Bumblebee), there is *FYI: this is more technical, and repetitively uses a cooking/Wrestling theme.* -### Ingredients +## Ingredients The following is needed for the wrecipe: 1. An ADS account and an ADS API key (make an account [here](https://ui.adsabs.harvard.edu/#user/account/register), and then go to User Settings -> Customize -> API Token) 2. A [Heroku account](http://herokuapp.com) 3. Python "unofficial ADS client" by Andy Casey (https://github.com/andycasey/ads) -### Step 1: Decide what your application should do +## Step 1: Decide what your application should do First, we decided to create an application that pits two authors against one another by comparing their publication metrics against each other. Second, apply the 90s-00s WWE/WWF theme.
- + WWE-style promotional graphic for the ADS Author Smackdown app concept
-### Step 2: Obtain the information you need from the ADS +## Step 2: Obtain the information you need from the ADS We wanted to compare two authors against each other, *reasonably* fairly. One possible approach is to just compare total citations of one author to another, but obviously this can lead to biases given that someone who works longer should have more citations, people who have more papers from collaborations will have more citations, etc. To get around this, we chose to use the RIQ, a metric that is meant to *fairly* compare two authors. You can read more about this metric [here](https://ui.adsabs.harvard.edu/#abs/2012PLoSO...746428P/abstract). Of course, there are problems with this metric too, but..... @@ -50,11 +50,11 @@ Once you have the relevant bibcodes, we need to ask the metrics end point for th The above is fairly simple, and so you could do it via curl requests as outlined in our [API help pages](https://github.com/adsabs/adsabs-dev-api), or write your own client in the language of your choice. -### Step 3: Dish out your logic in a web app +## Step 3: Dish out your logic in a web app Our application will receive two authors names, and return the RIQs of each author, which will then display the winner (and loser) on the front-end application. To do this, we built a back-end application using Python-Flask, and a front-end application written in JavaScript. If you want to see the full code, you can see the Flask backend [here](https://github.com/jonnybazookatone/authorsmackdown) and the JavaScript frontend [here](https://github.com/aholachek/smackdown). At this stage you can utilise your favourite web application, cgi-bins, ruby on rails, go-lang, etc. -### Step 4: Decide how to deliver your app to the public +## Step 4: Decide how to deliver your app to the public You can opt to host your application locally if you prefer, and there are a plethora of free options on the internet. To get things running quickly, we chose to host our application on Heroku app (http://herokuapp.com). You only need to do two things: @@ -63,11 +63,11 @@ You can opt to host your application locally if you prefer, and there are a plet *Note* If you use your own API token for an application that is available to other users, your rate limits will be consumed as normal, and may run out during a 24 hour period. If you believe your application deserves its own rate limits then feel free to tweet us [@adsabs](http://twitter.com/adsabs) or [contact us directly](adshelp@cfa.harvard.edu). -### Step 5: Leave to cool for 5 mins and add a cliché title +## Step 5: Leave to cool for 5 mins and add a cliché title
- + Screenshot of the Author Smackdown web application comparing two authors' publication metrics
diff --git a/_includes/_blogcontent/2016-03-16-open-access-and-nasa-data.md b/_includes/_blogcontent/2016-03-16-open-access-and-nasa-data.md index fabefedc..cddce35e 100644 --- a/_includes/_blogcontent/2016-03-16-open-access-and-nasa-data.md +++ b/_includes/_blogcontent/2016-03-16-open-access-and-nasa-data.md @@ -1,5 +1,5 @@ -
+NASA logo
NASA Astrophysics is, and has always been, a leader in providing open access to scientific data. With small exceptions, all data from NASA missions are publically available. Indeed NASA has also been the leader in creating systems to make the access of these data easy and useful. diff --git a/_includes/_blogcontent/2017-10-05-100M-citations.md b/_includes/_blogcontent/2017-10-05-100M-citations.md index c07e1418..43e064c4 100644 --- a/_includes/_blogcontent/2017-10-05-100M-citations.md +++ b/_includes/_blogcontent/2017-10-05-100M-citations.md @@ -6,15 +6,15 @@ The ADS has reached its 100,000,000th citation! We hit this milestone the last w Our citations database has doubled in roughly the last 6 years. The growth in citations is rapid: the number of citations in the database increased nearly five-fold in the last decade and by two orders of magnitude in the last two decades. - +Bar chart showing growth in ADS citation count over time, reaching 100 million citations The number of records in the database that have been cited at least once has also increased over the same timespan, though not as quickly as the number of citations. The number of records in physics and astronomy that have been cited at least once has nearly doubled in the last 8 years. The more rapid increase in the number of citations than in the number of papers being cited is more easily visualized by the figure below, and is best understood when thinking of the citation dataset as a network of papers connected by citations. The figure, originally published as figure 4 in "The ADS in the Information Age - Impact on Discovery" and using data from 1980--2006, shows the number of edges (or number of citations) as a function of the number of nodes (or records that have been cited). The nonlinear growth of the number of citations is evidence of network densification. - +Scatter plot showing nonlinear growth of citations versus cited records in ADS from 1980 to 2006 This is partly a consequence of the growth in the average number of references in a bibliography, seen in the figure below (originally figure 5 from the same publication). This trend has only increased since widespread adoption of electronic publishing in the late 1990s, seen as the upwards deviation from the linear trend in bibliography growth. - +Line chart showing growth in average number of references per bibliography in ADS publications over time The process by which a paper is cited in the ADS is not always obvious to our users. When a paper is ingested, the publisher-provided reference list is read. (For arXiv e-prints or other works without separate reference lists, the paper’s full text is scanned and references are extracted directly from the text.) Individual reference strings are recognized and the bibliographic tokens within them are parsed. We then attempt to match the parsed reference metadata against the existing records within ADS. When a possible match is found, we compute a similarity score between the parsed reference data and that of the potential match in ADS. If the similarity score is high enough, the reference is accepted and a reference/citation pair is created between the referencing paper and the cited paper. The citations table is formed by inverting the references table. The resulting citations table is then checked for duplicates, such as from previous versions of the citing paper that have appeared on the arXiv. diff --git a/_includes/_blogcontent/2017-12-12-adsug.md b/_includes/_blogcontent/2017-12-12-adsug.md index 439d630c..a07dc33e 100644 --- a/_includes/_blogcontent/2017-12-12-adsug.md +++ b/_includes/_blogcontent/2017-12-12-adsug.md @@ -5,27 +5,27 @@ One of the ADSUG members is Erick Peirson, lead system architect at arXiv. Erick Presentations and discussions at the main ADSUG meeting covered a lot of ground quickly over the two-day meeting. A full report is expected from the committee in the next month or so, but in the meantime, an overview of the major topics covered is given below, or check out the [online program](../../about/adsug/past_meetings/2018-01-01-201711-program). -### Removing the Beta from ADS Beta (a.k.a. Bumblebee) +## Removing the Beta from ADS Beta (a.k.a. Bumblebee) The ADS development team has been hard at work on [ADS Beta](https://ui.adsabs.harvard.edu/), codenamed Bumblebee, since 2015, an outgrowth of earlier efforts (ADS Labs, ADS 2.0) to modernize the interface, infrastructure, and search capabilities of ADS Classic. These development efforts are paying off and Bumblebee is now rapidly approaching feature and content parity with ADS Classic, a nearly 25-year-old system. In addition, Bumblebee provides a much richer search experience, including full-text searching for most recent publications, on-the-fly search filtering, and integration with systems such as ORCID. Full parity with Classic is expected to be reached in early 2018, and ADS Classic will be slowly phased out over the 6-12 months following that milestone. -### System architecture improvements +## System architecture improvements System architecture development in Bumblebee is multi-pronged. The development team reported on recent architecture development in several areas. First, Bumblebee is cloud-based, unlike ADS Classic, which is hosted in locally maintained servers and mirror servers. Scaling up the system to ensure a snappy response time thus requires different solutions, including testing [Kubernetes](https://kubernetes.io/) as a scalable deployment technology and other speed improvements. Second, ingesting data into the ADS databases relies on a series of pipelines to transform raw data from publishers and other sources into appropriately formatted and fielded metadata, to calculate citation data and other metrics, and to append other related information to a publication record. These pipelines are in the process of being re-engineered to improve speed and reliability. Third, the front-end interface of Bumblebee has been improved in a number of ways under-the-hood, including improved error handling. Finally, the dev team outlined future areas for improvements to the system architecture, all targeted at improving speed and reliability for users. -### Planetary sciences +## Planetary sciences After the [previous ADSUG meeting](../../about/adsug/past_meetings/2018-01-01-201701-program), the [committee recommended](http://ads.harvard.edu/adsug/2017/ADSUG_Report.pdf) that ADS investigate the effort involved in more thoroughly covering the planetary sciences literature. While much of the planetary sciences corpus is currently included in ADS, it’s technically out of the scope of ADS’s holdings and little effort has been expended to ensure its completeness. ADS reported on a preliminary study to explore what would be required to move the planetary sciences literature into our core holdings. While the study indicated that the move would be welcomed by the planetary sciences community, many of whom have astronomy backgrounds and are already familiar with ADS, it would require a good deal of effort on the part of ADS. The ADSUG is expected to make a recommendation on how ADS should follow up on this preliminary study. -### Software citations (Project Asclepias) +## Software citations (Project Asclepias) ADS, in collaboration with AAS and [Zenodo](https://zenodo.org), is working to improve citations to software products. Project [Asclepias](https://github.com/asclepias/) allows developers of astronomy-related software to upload their versioned code to an online repository such as Github, publish a released version in Zenodo, and receive a DOI for their code. The Zenodo DOI enables researchers to cite the appropriate version of the code directly, without resorting to hacks such as citing a published article describing the software. ADS will soon track the citations to these Zenodo DOIs, allowing researchers with a focus on software development to properly receive credit for their work. Asclepias will be reported on more thoroughly in an upcoming blog post. -### Affiliations and collaborations +## Affiliations and collaborations Author affiliations have long been included in ADS but successfully searching for an author by including their affiliation as a search term is non-trivial. This is in large part due to lack of consistency in how affiliations are recorded. To take ADS’s home institution as an example, an author could record their affiliation as “Center for Astrophysics,” “Harvard-Smithsonian Center for Astrophysics,” “CfA,” or one of many other variants. Mapping these variants to each other is a complex problem that we are solving by incorporating machine learning techniques. The implementation of this new feature is still underway, but will eventually allow users to more confidently search using author affiliations as a search term. A related issue is that of large collaborations, such as LIGO. For arXiv e-prints and conference proceedings, few authors explicitly list all members of large collaborations, instead generally listing the name of the collaboration itself and perhaps a small number of authors. (Published journal articles do generally include the full author lists.) Searching for a member of a given collaboration will thus fail to find any publications that are “authored” by the collaboration. In addition, similarly to author affiliation, there are many published variants of a given collaboration’s name (e.g. LIGO Scientific Collaboration vs. LIGO Collaboration). With the rise of more and larger collaborations and their prominence, ADS is exploring how best to resolve this issue. -### ORCID +## ORCID ORCID is a non-profit organization that issues ORCID IDs, a method of disambiguating authors, especially those with common names. [ADS has incorporated ORCID functionality into Bumblebee](../blog/orcid-claims), allowing authors to claim their papers. Papers with approved claims are then discoverable when searching by an author’s ORCID ID, allowing authors to maintain a personal bibliography. ADS is exploring methods for improving and expanding ORCID functionality within the system. -### Future directions +## Future directions We wrapped up the ADSUG meeting by discussing future directions with the committee, including some long-term possibilities for ADS. Based on our presentations and their own discussions, the ADSUG is currently preparing a report with their suggestions for current and future development; that report will be available on the [ADSUG page](../../about/adsug) when ready. We also welcome community input---if you’re interested in contributing to or serving on the ADSUG, contact the ADSUG chair or your nearest member! diff --git a/_includes/_blogcontent/2018-02-05-asclepias.md b/_includes/_blogcontent/2018-02-05-asclepias.md index 13fe305d..5f45d5d1 100644 --- a/_includes/_blogcontent/2018-02-05-asclepias.md +++ b/_includes/_blogcontent/2018-02-05-asclepias.md @@ -2,16 +2,36 @@ Soon, if not already, the research lifecycle will be fully digital. Every stage can be captured by one or more digital objects, each of which carries specific knowledge with regards to that stage. The most obvious inhabitant of this digital cosmos is the scholarly publication, but there are many more species, ranging from observation proposals, datasets, software to posters and presentations. With repositories like mission data archives, [Figshare](https://figshare.com/) and [Zenodo](https://zenodo.org/), all of these objects can, in principle, be made discoverable and citable. In this blog we focus on one particular digital object: software. Enter ***Asclepias***! Asclepias, “*Enabling software citation and discovery workflows*”, is a project funded through a grant from the Alfred P. Sloan Foundation to the American Astronomical Society (AAS), and it involves collaboration between the AAS, Zenodo, the ADS and Thomas Robitaille as freelancer. Why this collaboration? It reflects the fact that no one stakeholder can “solve” the problem of software citation.
- + Diagram showing the research life cycle stages from proposal through publication and data archiving Figure source: "Research Life Cycle" image from UC Irvine [Library Digital Scholarship Services](https://www.lib.uci.edu/dss)
-| | | -| :------------- |:-------------| -| AAS | Gus Muench | -| ADS | Alberto Accomazzi, Sergi Blanco-Cuaresma, Edwin Henneken | -| Zenodo | Lars Holm Nielsen, Krzysztof Nowak
, Alexander Ioannidis | -| Robitaille | Thomas Robitaille | + + + + + + + + + + + + + + + + + + + + + + + + + +
OrganizationTeam Members
AASGus Muench
ADSAlberto Accomazzi, Sergi Blanco-Cuaresma, Edwin Henneken
ZenodoLars Holm Nielsen, Krzysztof Nowak, Alexander Ioannidis
Thomas RobitailleThomas Robitaille
What is so special about software citation that it takes so many parties to deal with it properly? This becomes clear when you think about how to move from a position where the curation and preservation of software products has been taken care of, to one where these products are discoverable, together with their links to the scholarly literature (by means of citations or otherwise). One challenge is that currently, there is no established standard or policy for citing software in scholarly publications. Writing a “software paper” may seem like a work-around, but it is not a very good one. It can work if you just write one, static piece of software. You describe how it works, acknowledge contributors and, perhaps, where people can get a copy, and you’re done. In all other cases, even though it is better than nothing, a “software paper” is just a bad proxy for representing all aspects. Software is a highly dynamical object, especially when it evolves from version to version, with different contributors and different characteristics. For this reason, it is important to capture the acknowledgement of actual software products. Since reworking the entire, established process of capturing scholarly acknowledgement (read: “citations”) is extremely hard, to say the least, adapting the existing mechanism of finding citations to include software, will be the next best thing. @@ -20,23 +40,32 @@ This is exactly what the Asclepias project focuses on. Its goal is to **promote What does all of this mean in practice? Let’s look at an example. The Python module *corner.py* (previously known as *triangle.py*) is widely used in astronomy. Its main developer, Daniel Foreman-Mackey, made it available on [Github](https://github.com/dfm/corner.py) and published an [entry](http://joss.theoj.org/papers/10.21105/joss.00024) in the Journal of Open Source Software (JOSS). The ADS has a [record](http://ui.adsabs.harvard.edu/#abs/2016JOSS.2016...24F/abstract) for this JOSS software paper, and as a result citations are being captured (provided people cite this record properly). As of November 9, 2017, this JOSS paper accumulated 77 citations.
- + Screenshot of the ADS record for the corner.py JOSS software paper showing citation count
Thanks to Zenodo’s interoperability with Github, records were created for both *triangle.py* and *[corner.py](https://doi.org/10.5281/zenodo.53155)*. Zenodo mints a DOI for each software version and also a so-called concept DOI. The concept DOI is available for when you don’t want to cite a specific software version, but just “the latest”. The crucial step that make this interoperability possible is the authentication within Zenodo, using your Github account, allowing Zenodo to view and retrieve your repositories on Github. For details, see: https://guides.github.com/activities/citable-code/.
- + Screenshot of Zenodo record for the corner.py software package showing DOI and version metadata
The next step is to go through the reference data in the ADS holdings and see if we find any evidence of the Zenodo DOIs, corresponding with the different versions of both *triangle.py* and *corner.py*. The table below shows the results (as of Feburary 5, 2018). -| | | | -| ------------- |:-------------:| -----:| -| 10.5281/zenodo.10598 | triangle | 2 | -| 10.5281/zenodo.11020 | triangle | 40 | -| 10.5281/zenodo.45906 | corner | 16 | -| 10.5281/zenodo.53155 | corner | 7 | + + + + + + + + + + + + + + +
Zenodo DOIModuleCitations
10.5281/zenodo.10598triangle2
10.5281/zenodo.11020triangle40
10.5281/zenodo.45906corner16
10.5281/zenodo.53155corner7
This analysis shows that authors are already citing the different versions of both modules, but also that it results in a significant amount of additional citations! diff --git a/_includes/_blogcontent/2018-04-11-updates.md b/_includes/_blogcontent/2018-04-11-updates.md index 1543ecfd..a0d04171 100644 --- a/_includes/_blogcontent/2018-04-11-updates.md +++ b/_includes/_blogcontent/2018-04-11-updates.md @@ -1,7 +1,7 @@ We’ve released a major update to the new [ADS Bumblebee](https://ui.adsabs.harvard.edu/) interface this week! Some changes, such as the inclusion of a wider range of export formats, incorporate functionality from ADS Classic, while others improve the user’s site experience. Read on for more. -### Unfielded searches: now metadata-only +## Unfielded searches: now metadata-only In response to user feedback about differences in searching between Classic and Bumblebee, we’ve made some changes to the search functionality. Previously, searches made without the use of search terms, such as *author:* or *year:*, automatically searched both the metadata and full text (available for more than 4 million records, including most recent journal articles). However, searching the full text by default is non-intuitive for many users and can impede some common searches. For example, if a user is searching for an author name and a publication year without using search terms, such as *accomazzi 2001*, the default full text search will include matches based on references and other information within the text. Depending on the search terms, the full text search will generally return many more matches than searches based strictly on record metadata. @@ -10,7 +10,7 @@ Based on user feedback, we’ve adjusted the behavior of unfielded searches. (No It’s still possible to search the full text, for those records that have it available. To do so, use one of the full text search terms with your search term. *Body:* searches the body of the paper, while *full:* searches the body, title, abstract, keywords, and acknowledgements sections. Example full text searches include *body:“hubble space telescope”* or *full:“hubble space telescope”*. -### Sort options +## Sort options The sort buttons have been revamped, with the sort field selection now separated from a button that switches between descending and ascending order. New sort options are also available. While the default sort is based on publication date, two sort options may be useful for users interested in sorting based on relevance. **Score** @@ -21,7 +21,7 @@ Behind the scenes, some fields are weighted to prioritize more commonly searched The classic factor sorts based on a prestige score, designed to more highly rank papers that are relevant and popular now. The classic factor is calculated via an age-normalized combination of reads and citations; it is very similar to the ranking applied to results from [Classic’s one-box search](http://adsabs.harvard.edu/). -### Author Affiliation form +## Author Affiliation form The author affiliation form, found on the **Export** menu at the top right on the search results page, is designed to assist users supply a list of co-authors for grants and other applications. author affiliation link on export menu @@ -30,18 +30,18 @@ Users seeking to create such a list should begin with an author search and then author affiliation form -### Export formats +## Export formats More export formats have been added, covering a range of formats required by astrophysics journals. From the **Export** menu, select **Other Formats** to be taken to the export page. Select the appropriate export format from the menu and click Apply to see the results displayed. The formatted records can be copied to the clipboard or saved to file. -### ORCID improvements +## ORCID improvements Several improvements have been made to our ORCID system, including an upgrade to use the ORCID v.2 API. Users are now able to claim and delete multiple records at a time. After [signing into ORCID in ADS](../help/orcid/claiming-papers), select the relevant records in the search results and use the ORCID Bulk Actions box on the right-hand side to claim or delete the selected records. In addition, improvements have been made for speed and efficiency, which will especially affect users with many claimed records. ORCID bulk action selection in the righthand column of the search results page -### Speed and efficiency improvements +## Speed and efficiency improvements Several adjustments have been made to the user interface to improve page loading speeds. Overall, Bumblebee should load faster to start and navigate between pages more quickly. -### About page +## About page An [About page](https://ui.adsabs.harvard.edu/about/) is now available from the top navigation bar. Read about [our team](https://ui.adsabs.harvard.edu/about/team/), [the history of ADS](https://ui.adsabs.harvard.edu/about/history/), and more.
diff --git a/_includes/_blogcontent/2018-05-24-transition.md b/_includes/_blogcontent/2018-05-24-transition.md index 3a402f04..c58315eb 100644 --- a/_includes/_blogcontent/2018-05-24-transition.md +++ b/_includes/_blogcontent/2018-05-24-transition.md @@ -1,8 +1,8 @@ -### Update (April 12, 2019) +## Update (April 12, 2019) Classic's retirement timeline has been adjusted slightly. We plan to begin disabling searching in Classic in May 2019, with full site retirement slated for Q3 2019. For more on steps to take before that time, see [our post on things to do before the transition](../blog/transition-reminder). -### Original post +## Original post ADS is excited to announce that the [new ADS interface](https://ui.adsabs.harvard.edu/), codenamed Bumblebee, is leaving its beta label behind! The service, under development since 2015, has reached parity with ADS Classic. In addition, it provides a modern interface and new search features. ADS Classic, in service since 1994, will be phased out over the next year and will be retired on May 31, 2019. While it has served its original purpose well, still serving roughly 50,000 unique users a day and around three-quarters of a million unique users a month, Classic’s 90s-era infrastructure makes it impossible to continue to scale and to incorporate more modern search features. (For the curious, check out our [more technical post](../blog/technical) about what’s under the hood of both Classic and Bumblebee.) diff --git a/_includes/_blogcontent/2018-07-17-concepts-at-work.md b/_includes/_blogcontent/2018-07-17-concepts-at-work.md index ad4d780b..686e7ab9 100644 --- a/_includes/_blogcontent/2018-07-17-concepts-at-work.md +++ b/_includes/_blogcontent/2018-07-17-concepts-at-work.md @@ -8,7 +8,7 @@ Authors publish because they want to transfer information. They have been doing The research project "Concepts at work" was originally developed in a workshop which planned a long term investigation into astrophysics research practices in the light of philosophical, sociological and historical questions. Inspired by the epistemology of Polish immunologist Ludwik Fleck (1896–1961) (Fleck, 1979), this multidisciplinary enterprise was fixed to study how astrophysical facts come into being and evolve.
- + Portrait photograph of Ludwik Fleck, Polish immunologist and epistemologist (1896-1961)
Ludwik Fleck (credit: Archiv für Zeitgeschichte Zürich)

@@ -17,7 +17,7 @@ The historical project which was granted a three year funding by the DFG (German In the project at hand, [Karin Pelte](http://www.philosophie.tu-berlin.de/menue/fachgebiete/wissenschaftsgeschichte/team/wissenschaftliche_mitarbeiter/karin_pelte_ma/) studies the world wide development of the research on multiple and interacting galaxies from around 1925 to 1980. *Multiple and interacting galaxies* (MIG from here on) is used as a catch-all and represents many of the names given to such phenomena as double, binary, multiple, colliding, merging, exploding, satellite galaxies, or small groups and chains or nests of galaxies.
- + Page from Vorontsov-Vel'yaminov's 1977 Atlas and Catalogue of Interacting Galaxies showing galaxy images Taken from Vorontsov-Vel'yaminov's Atlas and Catalogue of Interacting Galaxies II, 1977

diff --git a/_includes/_blogcontent/2018-08-20-citations-journals.md b/_includes/_blogcontent/2018-08-20-citations-journals.md index 383735a3..a1cf0675 100644 --- a/_includes/_blogcontent/2018-08-20-citations-journals.md +++ b/_includes/_blogcontent/2018-08-20-citations-journals.md @@ -22,7 +22,7 @@ We have also run the query on all refereed articles in the ADS; - + Line chart showing growth in astronomy paper counts from 1997 to 2016 for in-sample and out-of-sample journal sets Figure 1
@@ -34,7 +34,7 @@ The In Sample group shows a steady 4% yearly increase in number of papers publis Most of the Out of Sample journal articles are not from small astronomy journals (this has been steadily declining from about 10% to about 3% now); instead, they are from nearby physics/geophysics related disciplines. Assuming these fields are not growing any faster than the 4% rate of astronomy (or all science) we can conclude that the interdisciplinary reach of astronomy is growing by about 2.7% per year, a 25 year doubling period. As a percentage, the Out of Sample papers grew from 25% to 40% of the total during the 20 year period.
- + Line chart showing total citation counts by publication year for in-sample and out-of-sample astronomy journals Figure 2

diff --git a/_includes/_blogcontent/2018-10-22-citations-journals-2.md b/_includes/_blogcontent/2018-10-22-citations-journals-2.md index 2c1d2967..2142675a 100644 --- a/_includes/_blogcontent/2018-10-22-citations-journals-2.md +++ b/_includes/_blogcontent/2018-10-22-citations-journals-2.md @@ -1,7 +1,7 @@ This is the second of a series of blog posts measuring the journals that publish astronomy research articles, using citation statistics with a number of different indices. In this post, we examine the performance of individual journals with respect to each other over time. We use the data described and published in [Part 1](../blog/citations-journals), which looked at some of the integrated properties of the sample, such as citation counts and h-indices. In Part 3, we will look into some of the properties of the indices. -### A. Ranked Lists +## A. Ranked Lists We begin by creating ranked lists of the 50 journals in the main sample for each of the 5 bibliometric indicators: number of articles, number of citations to these articles, h (Hirsch) index, i10 (number of articles with 10 or more citations), and i100 (number of articles with 100 or more citations). We do this for each of the 20 years (1997-2016) of the study. The appendix, [published on Zenodo (DOI: 10.5281/zenodo.1400692)](https://doi.org/10.5281/zenodo.1400692), contains all the lists. Much can be gleaned from these lists; we recommend the reader avails themself of this opportunity. We will illustrate some of the results by a little cherry picking. @@ -28,7 +28,7 @@ There are (at least) three main takeaways from looking at these lists: 3. The physics journals have substantially increased their role in astrophysics research. In 1997 the only physics journal in the top 10 is PhRvD at #10, twenty years later there are 5 (counting JCAP as physics), with PhRvD at #4. Remember that this is for only those papers which are “astronomy related” as described in Part 1; they are a fraction of the papers published by these journals. For example in 2016 9% of the papers in PhRvL were astronomy related, as were 29% of the papers in PhLB. -### B. Winners and Losers +## B. Winners and Losers As shown in Figure 1 of [Part 1](../blog/citations-journals), the astronomy literature has been growing over the past two decades. While astronomy has spread its influence into related areas (and this is the point of that figure), the core astronomy literature can be taken as being within the ~50 major international journals of physics, astrophysics, and geophysics in our main sample (listed in Part 1). The growth of this literature has been a steady 4% per year, doubling over the period, consistent with long term trends in many disciplines. @@ -39,13 +39,13 @@ Figure 1 of this post shows the three “winners”: MNRAS, PhRvD, and JCAP, as Figure 2 shows the three “losers”: A&A, ApJL, and AJ, also with the ApJ as a fiducial. A&AS was merged into the main journal in 2001; the A&A line represents the sum. All three journals lost about half their market share during the last two decades.
- + Line chart showing market share gains for MNRAS, PhRvD, and JCAP compared to ApJ from 1997 to 2016 Figure 1

- + Line chart showing market share losses for A&A, ApJL, and AJ compared to ApJ from 1997 to 2016 Figure 2

@@ -57,7 +57,7 @@ Note that the number of citations is as measured in the middle of July 2018; eac Looking at Figure 3, the first thing to notice is the decline in mind share for the Astrophysical Journal. The ApJ had an extraordinary presence 20 years ago, with nearly a quarter of all citations to astronomy related papers on somewhat less than a sixth of the total astronomy related papers. Now, the ApJ still has somewhat less than a sixth of the total papers but only slightly more than a sixth of the total citations (and thus mind share).
- + Line chart showing mind share trends for MNRAS, PhRvD, and JCAP compared to declining ApJ from 1997 to 2016 Figure 3

@@ -76,7 +76,7 @@ Were they to be gaining market share by lowering their standards, the slopes for Figure 4 shows the changes in mind share for the three journals that are the biggest losers in terms of market share (again with the ApJ as a fiducial). Were they to have lost market share by raising their standards, we would expect to see declines in mind share that are less steep than in market share. We do see that for A&A, while the ApJL mind share slope is the same as the market share slope, and the AJ mind share decline is even steeper than its market share decline.
- + Line chart showing mind share changes for A&A, ApJL, and AJ compared to ApJ, showing A&A improving relative to market share Figure 4

diff --git a/_includes/_blogcontent/2019-02-13-updates2.md b/_includes/_blogcontent/2019-02-13-updates2.md index 393e48bd..e187617f 100644 --- a/_includes/_blogcontent/2019-02-13-updates2.md +++ b/_includes/_blogcontent/2019-02-13-updates2.md @@ -1,19 +1,19 @@ -We’ve rolled out a number of changes to the new ADS over the summer and fall, some of which you’ve likely noticed and others which may have passed you by. Read on for a summary of some of the bigger updates. If you want to stay up to date on changes with ADS, [sign up](http://eepurl.com/ggoxhn) for our monthly newsletter or check in occasionally with our [What’s New page](../help/whats_new/). +We’ve rolled out a number of changes to the new ADS over the summer and fall, some of which you’ve likely noticed and others which may have passed you by. Read on for a summary of some of the bigger updates. If you want to stay up to date on changes with ADS, [sign up](https://eepurl.com/ggoxhn) for our monthly newsletter or check in occasionally with our [What’s New page](../help/whats_new/). -### Application settings +## Application settings [New settings related to the user interface](https://ui.adsabs.harvard.edu/#user/settings/application) are now available if you have a user account in the new system. Options include: * Set a default database(s) to search in, e.g. you can choose to only search in the astronomy collection by default * Show or hide the left and right sidebars by default * Select a default export format other than BibTeX or create your own [custom format](../help/actions/export) to use later
- + Screenshot of ADS application settings page showing options for default database and sidebar visibility Application Settings within the user account

-### Interface changes +## Interface changes Some changes have been made to default behavior and to how the web interface responds to users: * Remove the left and right columns temporarily by clicking the Hide Sidebars button at the top of the search results. To disable the sidebars more permanently, set the option in your Application Settings (see above). * By default, any filters selected in the left-hand column will remain in effect if the query in the search bar on the search results page is edited and rerun. To remove any selected facets that are no longer relevant, click the X on the facet bubble just underneath the search bar. To remove all facets or filters (other than the default database specified in your Application Settings, as described above), click the Start New Search button in the upper left. @@ -21,28 +21,28 @@ Some changes have been made to default behavior and to how the web interface res * If you click through to an abstract page from the search results, clicking the Back button will now return you to the result you clicked on, instead of the top of the page.
- + Animated screenshot showing how to hide the left and right sidebars in ADS search results The left and right sidebars can be hidden as needed.

-### Affiliations filter +## Affiliations filter A new facet is available in the left-side column: affiliations. The result of a long-term project by our curation staff, it lists the disambiguated affiliations of authors in the search results. This gives an alternative for searching for *aff:STScI OR aff:“Space Telescope Science Institute”* or something similar; using the left-side column to filter on STScI will automatically find a curated set of related affiliations for you. This is similar to how the object filter currently works. We are still working on improving affiliation searching and filtering---keep an eye out for a future blog post on this exciting project! -### Software citations using Zenodo via project Asclepias +## Software citations using Zenodo via project Asclepias ADS now indexes software and its citations for projects archived on Zenodo and cited at least once by an ADS-indexed refereed paper ([AAS Nova announcement](https://aasnova.org/2019/02/04/what-should-astronomers-do-with-their-software/), [Zenodo announcement](http://blog.zenodo.org/2019/01/10/2019-01-10-asclepias/), [ADS blog post](../blog/asclepias)). Previously, software was only indexed by ADS if it was included in the Astronomy Source Code Library. Indexing software projects in Zenodo allows us to include software that is used by astronomers and other researchers but that may not be explicitly astronomy-related, such as statistics or plotting codes. Zenodo also allows different releases of software projects to be indexed and cited separately, useful if the code is significantly modified or if authorship has changed. Citations in ADS will accrue to each individual release as appropriate, and eventually “roll-up” functionality will be added so citations to all releases can be seen together. Instructions on getting your software into Zenodo and indexed in ADS can be found on [our help pages](../help/data_faq/#q-how-can-i-get-my-software-package-indexed-in-ads). -### Similar() operator +## Similar() operator The similar() operator looks for articles and other records that are semantically similar to the results from the query inside the parentheses. This is useful enough when looking for papers similar to an individual paper of interest, such as the initial discovery paper for GW150914, [similar(2016PhRvL.116f1102A)](https://ui.adsabs.harvard.edu/#search/q=similar(2016PhRvL.116f1102A%20)&sort=score%20desc%2C%20bibcode%20desc&p_=0). The search results for this query include the discovery papers for other gravitational wave detections and other useful papers. The operator’s real power comes when combined with other searches. For example, here we’ve added to the above search a filter to find papers published in arXiv in the past week: [similar(2016PhRvL.116f1102A) bibstem:arXiv entdate:[2019-02-06 TO 2019-02-13]](https://ui.adsabs.harvard.edu/#search/q=similar(2016PhRvL.116f1102A)%20bibstem%3A%22arxiv%22%20entdate%3A%5B2019-02-06%20TO%202019-02-13%5D&sort=score%20desc%2C%20bibcode%20desc&p_=0). This returns new papers that may be especially relevant for a researcher working in this field. Searching for your or another person’s name with the operator, following the syntax *similar(author:“Name”)* returns papers by those doing similar work, useful for finding potential collaborators or advisors. Wrapping a keyword query in the similar() operator, such as [similar(abs:“exoplanet atmospheres”)](https://qa.adsabs.harvard.edu/#search/filter_database_fq_database=AND&filter_database_fq_database=database%3A%22astronomy%22&fq=%7B!type%3Daqp%20v%3D%24fq_database%7D&fq_database=(database%3A%22astronomy%22)&q=similar(abs%3A%22exoplanet%20atmospheres%22)&sort=score%20desc%2C%20bibcode%20desc&p_=0) will find related papers that the initial search may have missed. A quick note: Searches using the similar() operator are computationally intensive, so will take longer than usual to return results. -### Libraries +## Libraries New sorting options have been added to more easily parse the contents of a library, and the new bulk delete function makes it simple to delete multiple records from a library. More improvements are planned for the libraries in 2019, so keep an eye out. -### Quicker posting of new arXiv records +## Quicker posting of new arXiv records Previously, new [arXiv](https://arxiv.org/) records took up to a day to be indexed in the new ADS, which meant that it was sometimes a day behind Classic’s arXiv listings. Now new arXiv papers are generally ingested and available in the new ADS the same day they’re available on arXiv.
diff --git a/_includes/_blogcontent/2019-03-26-citations-journals-3.md b/_includes/_blogcontent/2019-03-26-citations-journals-3.md index c4858633..539caa90 100644 --- a/_includes/_blogcontent/2019-03-26-citations-journals-3.md +++ b/_includes/_blogcontent/2019-03-26-citations-journals-3.md @@ -12,7 +12,7 @@ The [Journal Impact Factor](https://ui.adsabs.harvard.edu/#abs/1972Sci...178..47 Impact is a form of relative aging. In the case of scholarly articles, aging is often measured by counting citations. As material ages, in general we observe relative decrease in its use, translating into decreasing citation counts. In bibliometrics we refer to this effect as the obsolescence of citations. Qualitatively speaking, the effect is the same across all journals, but there are differences on a quantitative level: relative use differs among journals and in that sense a given journal's impact is different. Traditional impact measures overlook these longer-term effects. Here we present two different ways to examine these obsolescence effects. First we ask the question: given the references in astronomy articles published in the set of 50 journals in year Y, what fraction of (astronomy content of) journal J is cited in year Y-n? The diagram below present these fractions based on 2017.
- + Line chart showing fraction of astronomy journal articles cited by year, comparing ApJ, MNRAS, A&A, and ApJS Figure 1

@@ -28,7 +28,7 @@ IF(Y,n) = num total cites to astronomy articles published in year Y in the n yea This IF is another way of quantifying relative aging of citations, or relative use of articles. The diagram below shows a comparison between MNRAS, A&A, and the ApJ (main journal). The dotted line represents equal IF between the ApJ and a given journal. Qualitatively IF ratios grow linearly for the journals in our comparison below (R2=0.9996). However, quantitatively speaking, the MNRAS values of IF are about 0.72 of those for the ApJ for publications from 1997. In the case of A&A articles published in 1997, the IF values are 0.57 of those for the ApJ. In addition to articles published in 1997 (black points), the diagram compares IF values for articles published in 2002 (purple points), 2007 (green points), and 2012 (orange points). For each journal and publication year, a line has been fit to the data, as shown. For 2002 the slope for MNRAS increased to 0.74 and for A&A to 0.61. Again 5 years later, we only see a significant increase for A&A, but the size of the ApJ is still significantly larger. This illustrates the dominance of the ApJ in the field. These shifts in time are due to multiple factors that will be hard to single out. For one, editorial policies change over time. We also know that citation behavior changes over time (see e.g. [Henneken et al. 2009](https://ui.adsabs.harvard.edu/#abs/2009JInfo...3....1H/abstract), figure 2). We do see the effect we mentioned in the [previous blog](../blog/citations-journals-2), of MNRAS catching up with the ApJ. This is illustrated by the data for 2016.
- + Scatter plot comparing impact factor ratios of MNRAS and A&A relative to ApJ for publications from 1997 to 2012 Figure 2

@@ -36,7 +36,7 @@ This IF is another way of quantifying relative aging of citations, or relative u We offer one last way of comparing journals: compare mean cites for astronomy papers relative to mean cites in the Sample Group (consisting of the 50 journals, defined in the [first blog](../blog/citations-journals)). Here we may look at "Letter journals" and "Regular journals" separately, because these are different classes in terms of citation rates.
- + Line chart showing mean citations per article relative to sample group mean for letter and regular astronomy journals Figure 3

@@ -44,7 +44,7 @@ We offer one last way of comparing journals: compare mean cites for astronomy pa The relatively steep rise for PhRvL is largely due to gravitational wave publications, especially the LIGO papers, just like how the Planck papers skew the results for A&A (see diagram below). Values for 2017, and probably even 2016, should be interpreted with some caution, because these publications are still actively accumulating significant citations. It is also worth noting that a journal like E&PSL is very much embedded in the Earth Sciences discipline, which has very different citation rates.
- + Line chart showing mean citations per article for selected journals including PhRvL and A&A, highlighting Planck paper effect Figure 4

diff --git a/_includes/_blogcontent/2019-04-11-transition-reminder.md b/_includes/_blogcontent/2019-04-11-transition-reminder.md index e328d4e4..4fbea18b 100644 --- a/_includes/_blogcontent/2019-04-11-transition-reminder.md +++ b/_includes/_blogcontent/2019-04-11-transition-reminder.md @@ -1,8 +1,8 @@ -### Update (September 11, 2019) +## Update (September 11, 2019) *This post has been updated with the latest schedule. Some links have been updated.* -### Update (May 29, 2019) +## Update (May 29, 2019) *This post has been updated to reflect that the library set operations and the "perform actions on selected articles" functionality, previously listed in the "Classic features in progress" section, are now available.* ADS Classic, [online since 1994](https://ui.adsabs.harvard.edu/about/history/), will be retired at the end of October 2019. (For more on the technical need for this upgrade, see [this previous blog post](../blog/technical).) Regular Classic users may have noticed some changes over the last few months, including an increasing number of warnings and pointers to the [new ADS](https://ui.adsabs.harvard.edu/), meant to encourage users to begin routinely using the new interface. As of the date of this post, Classic is still available, though its remaining time is limited. Now is an excellent time for the remaining Classic users to begin to familiarize themselves with the new system and to [contact us](mailto:adshelp@cfa.harvard.edu) if they run into problems. Below, we list a few important things for users to know as they begin to use the new ADS. @@ -23,7 +23,7 @@ The new ADS and Classic have separate user databases, which means that user acco As with user accounts, libraries in Classic and the new ADS are stored in different databases and will not be transferred automatically. However, we do offer a tool to help import libraries from the old system into the new one. After creating a new user account and logging in, users can link their old account to their new one and [import their libraries](../help/libraries/legacy-importing) using the import tool. There are several things to note about the import tool: all libraries in the old account will be imported, though unwanted libraries may be deleted after import. Also, the tool imports libraries, it does not link them, so changes made to libraries in the old system after import will not propagate to the new one. Other guidelines for using this tool can be found on the [help page](../help/libraries/legacy-importing).
- + Import Classic libraries into the new ADS interface Import Classic libraries into the new ADS

@@ -34,7 +34,7 @@ Users with an account in the new ADS have access to settings that allow them to In addition to the library link server, users with accounts can set some [application settings](https://ui.adsabs.harvard.edu/user/settings/application). These include setting a default database(s) or collection(s) for searches, such as limiting results to astronomy only by default; automatically hiding the left and right sidebars on the search results page; and defining custom formats for exporting citations.
- + ADS application settings page showing customization options Application settings

@@ -53,7 +53,7 @@ These features were previously listed as "in-progress" but are now available in - Perform actions on selected articles: Second order operations, such as retrieving the references of selected articles, are now available for a subset of articles manually selected from the search results set. To access this feature, select the desired articles in the search results, then click the Explore menu and choose the desired operation
- + Animated demo of performing actions on selected articles in the new ADS Performing actions on selected articles in the new ADS

diff --git a/_includes/_blogcontent/2019-05-30-ave-atque-vale.md b/_includes/_blogcontent/2019-05-30-ave-atque-vale.md index 354297a7..73cfc5ee 100644 --- a/_includes/_blogcontent/2019-05-30-ave-atque-vale.md +++ b/_includes/_blogcontent/2019-05-30-ave-atque-vale.md @@ -4,7 +4,7 @@ ADS Classic, a pioneer of the Information Age, died at 3:19 pm EDT on 30 May 201 Conceived near the dawn of the internet era, and born, following a difficult gestation, after the first cup of coffee, the Abstract Service, as it was then called, had many parents. In approximate time order: Michael Kurtz, Joyce Rey-Watson, Geoff Shaw, Peter Ossorio, Steve Murray, Guenther Riegler, Frank Giovane, Margaret Geller, Guenther Eichhorn, Todd Karakashian, Carolyn Stern Grant, and Alberto Accomazzi.
- + Screenshot of ADS Classic interface at the time of its birth in the early 1990sScreenshot of ADS Classic interface at the time of its retirement in 2019 ADS Classic at the time of its birth, and at the time of its death.

diff --git a/_includes/_blogcontent/2020-01-15-affiliations-feature.md b/_includes/_blogcontent/2020-01-15-affiliations-feature.md index 94b5c410..b6469b9b 100644 --- a/_includes/_blogcontent/2020-01-15-affiliations-feature.md +++ b/_includes/_blogcontent/2020-01-15-affiliations-feature.md @@ -3,12 +3,12 @@ One of the features new to ADS since the new interface has launched is search an Users are reminded that while affiliation information is largely complete for recent refereed literature, not all records contain an affiliation, therefore, searching by affiliation alone will inherently be incomplete. We strongly recommend combining affiliation searches with author searches for best results. -### Using affiliations as part of your search strategy: Author searches and the Affiliation facet +## Using affiliations as part of your search strategy: Author searches and the Affiliation facet Affiliation data for papers are available via the "Affiliations" facet in ADS. As an example, if you search for a first author, you'll get a list of papers having that first author, and on the left-hand side of the results page you'll see ways to refine those results -- who their coauthors are, whether the paper is in the astronomy, physics, or general database, whether it's a refereed publication or not, and so on. One of those facets is "Affiliations", and by clicking it you'll get a list of institutional affiliations sorted by the number of papers having that affiliation.
- +Screenshot of the ADS Affiliations facet showing institutional affiliations sorted by number of papers
Example of the Affiliations facet
@@ -16,7 +16,7 @@ Affiliation data for papers are available via the "Affiliations" facet in ADS. Using one of this blog's coauthors, searching for first_author:“Templeton, Matthew" brings up a list of his papers along with a few other "Matthew Templeton"s who are active researchers in ADS-relevant fields. Selecting the "astronomy" collection and "limit to" yields (mostly) just his set of first-authored publications, and refereed lowers it further to a manageable number. If you then open the Affiliations facet, you're presented with a list of all affiliations (of any author) contained within his papers. Matthew Templeton's historical affiliations -- AAVSO, New Mexico State University, Yale University, Los Alamos National Laboratory -- are among the most common in the list. However, you also find affiliations of co-authors too, for example Iowa State and the Center for Astrophysics. -### Using affiliations as part of your search strategy: Direct affiliation searches +## Using affiliations as part of your search strategy: Direct affiliation searches Affiliations in the ADS have been indexed in several different fields, with the intention of allowing multiple use cases. We have currently assigned identifiers with parent/child relationships, such as an academic department within a university. A child may have multiple parents, but we restrict a child from having children of its own. This has required a few modifications to remain useful. For instance, so that University of California schools can identify departments, we have assigned them a parent status, even though the "University of California System" should really be the parent level. Likewise, NASA's Goddard Space Flight Center is at a parent level, as are France's CNRS institutions to allow for further subdivision. Further work on a schema to allow more complex relationships between institutions is under development in conjunction with work by the [ROR Community](https://ror.org/). @@ -32,7 +32,7 @@ In addition to this new field, we've maintained the original search terms for af So, you could search for [aff:Harvard](https://ui.adsabs.harvard.edu/search/fl=identifier&q=aff:"Harvard") and get back all affiliations that contain Harvard in the affiliation string -- including "Harvard Street". To ensure you get only the University, you could search for [aff:“Harvard University"](https://ui.adsabs.harvard.edu/search/fl=identifier&q=aff:"Harvard%20University") but that would return only affiliation strings with that exact phrase, excluding "Harvard Univ.", "Harvard U", etc. Better would be to use the identifier for Harvard University by searching [aff_id:A00211](https://ui.adsabs.harvard.edu/search/fl=identifier&q=aff_id:A00211). This returns all affiliations which contain Harvard University at the parent level. Best yet would be to search by institution, [inst:“Harvard U"](https://ui.adsabs.harvard.edu/search/fl=identifier&q=inst:"Harvard U") which returns affiliations which contain Harvard University at the parent level, plus all affiliations for all of Harvard University's children. -### How we got here: the curation and pipeline process +## How we got here: the curation and pipeline process **The human element: curation** @@ -55,7 +55,7 @@ We've entirely automated the process, so once the dictionary of affiliation stri However, we're getting close to the limit of what we can do with human classification without lots of effort. Our most recent pass through our metadata has just over 4.8 million unique unclassified strings yielding a total of 16.6 million unclassified affiliations. There are about 6000 unclassified affiliations that appear 100 times or more in the metadata and assigning them aff_ids would provide a lot of new information. However, over 65 percent of unclassified affiliations occur fewer than 10 times, and **13 percent of unmatched affiliation strings only appear once in all of our affiliation metadata**.
- + Chart showing nearly 90% of matched affiliation strings appear at least 10 times in the ADS databaseChart showing unmatched affiliation string counts dominated by those appearing fewer than 10 times Left: Nearly 90 percent of matched publisher-provided affiliation strings in our database appear at least 10 times. Right: The number of unmatched affiliation strings is dominated by those appearing fewer than 10 times.

@@ -66,6 +66,6 @@ We've found the process is reliable to the limits of the input dictionary, and a For now, we're using machine learning to assist with curation, but we're not yet confident enough to pass it an affiliation string and guarantee it returns the correct ID; it's not (yet) a part of our hands-off pipeline. It's an ongoing process of improvement, and always will be as new metadata keeps coming in. -### What's next? +## What's next? Searching ADS by affiliation is already very useful for helping with disambiguation, and for helping build institutional publication lists. We hope to make it even more powerful by integrating our system with [ROR](https://ror.org) and integrating publisher-specific identifiers in our workflow. We are actively working with other projects to extend ROR identifiers (which are assigned one per institution) to the department level. In addition, we hope to improve the user experience by coupling affiliation with authors, adding hover-over expansion of abbreviations, and implementing auto-complete with the institution search. As always, we welcome feedback and corrections. diff --git a/_includes/_blogcontent/2020-04-06-nasa-open-access.md b/_includes/_blogcontent/2020-04-06-nasa-open-access.md index 22a9be60..522a5c8f 100644 --- a/_includes/_blogcontent/2020-04-06-nasa-open-access.md +++ b/_includes/_blogcontent/2020-04-06-nasa-open-access.md @@ -67,7 +67,7 @@ elsevier/NASA | [380](https://ui.adsabs.harvard.edu/search/q=(aff%3ANASA%20OR%20
- +Bar chart showing open access percentages for NASA-affiliated research papers across publisher groups in 2018 Figure 1

diff --git a/_includes/_blogcontent/2020-05-29-ui-updates.md b/_includes/_blogcontent/2020-05-29-ui-updates.md index c56964f1..df965103 100644 --- a/_includes/_blogcontent/2020-05-29-ui-updates.md +++ b/_includes/_blogcontent/2020-05-29-ui-updates.md @@ -7,7 +7,7 @@ The myADS service, which notifies subscribers via email about new papers relevan The [setup page](https://ui.adsabs.harvard.edu/user/settings/myads) can be found within your account settings. Here, you can either set up new notifications, or if you were a subscriber of the Classic myADS notifications, you can import your existing settings from Classic.
- + Screenshot of the myADS setup page showing notification configuration options myADS setup

@@ -22,7 +22,7 @@ One of the most-requested features for ADS libraries has now arrived: the abilit * Read: A user with read privileges can view a private library.
- + Screenshot of the Manage Library Collaborators screen showing permission levels Manage Library Collaborators screen

@@ -40,7 +40,7 @@ The new score sort is ideal for these types of searches. The score sort is simil A search for Nobel Prize-winning astronomer Adam Riess shows the difference. Searching by his last name and sorting by date ([Riess](https://ui.adsabs.harvard.edu/search/q=Riess&sort=date%20desc%2C%20bibcode%20desc&p_=0)) returns the most recent papers first; some of these likely cite him in the abstract, include him or someone with the same name as *Nth* author, or otherwise mention his name in passing. Changing the sort to score order ([Riess](https://ui.adsabs.harvard.edu/search/p_=0&q=Riess&sort=score%20desc%2C%20bibcode%20desc)), however, returns his Nobel Prize-winning papers, and other highly cited works, at the top of the list.
- + Search results showing sort by score order, placing a Nobel Prize paper at the top Example of sorting by score

diff --git a/_includes/_blogcontent/2020-08-10-the_new_myADS.md b/_includes/_blogcontent/2020-08-10-the_new_myADS.md index 68c36fd3..2d0dd734 100644 --- a/_includes/_blogcontent/2020-08-10-the_new_myADS.md +++ b/_includes/_blogcontent/2020-08-10-the_new_myADS.md @@ -13,7 +13,7 @@ myADS provides four main types of notifications: - Keywords: Follow the most popular, recent, and cited papers that match a certain list of keywords (e.g., *gravitational waves OR cosmic microwave background*).
- + Screenshot of the myADS email notification settings page in ADS Example of myADS email notification settings

@@ -21,7 +21,7 @@ myADS provides four main types of notifications: No matter how many notifications you setup, they will be grouped together into a single daily or weekly email.
- + Example of a myADS weekly digest email showing grouped paper notifications Example of a myADS weekly email

@@ -29,7 +29,7 @@ No matter how many notifications you setup, they will be grouped together into a These alerts cover many of the typical use cases, but the new myADS is ready to unleash the full ADS potential by allowing fully customizable notifications. Now, any valid ADS search query can be converted into a daily or weekly notification.
- + Screenshot showing how to create a custom myADS notification from the ADS search results page Create general myADS notifications from the ADS results page

diff --git a/_includes/_blogcontent/2021-04-15-affils-update.md b/_includes/_blogcontent/2021-04-15-affils-update.md index c42b6450..433b48b6 100644 --- a/_includes/_blogcontent/2021-04-15-affils-update.md +++ b/_includes/_blogcontent/2021-04-15-affils-update.md @@ -3,7 +3,7 @@ We publicly introduced our affiliations feature in a [blog post](../blog/affilia Users should note that while affiliation information is more than 80% complete across all literature, not all records contain an affiliation. We strongly recommend combining affiliation searches with author searches for best results. -### What are Affiliations? +## What are Affiliations? An affiliation is whatever metadata a bibliographic record contains listing a contributing author's institutional location and/or membership(s). In nearly all modern literature, affiliation metadata is specifically fielded as such by publishers, and can be extracted, tagged, and made available for search. The ADS has always maintained affiliation data as a separate field within records and we encourage authors and publishers to include this with their author metadata. What has changed has been the inclusion of affiliation as a searchable field, and the assignment of unique identifiers to individual affiliation strings to improve their discoverability. @@ -13,28 +13,28 @@ The ADS has developed a curated database of affiliation identifiers where we hav These identifiers power our affiliation search feature, allowing you to search and select literature on the basis of affiliation data. With the ADS, you have two ways to use affiliation data in your searches: through the affiliation search filter, and directly in your search queries. We show you how below. -### Using affiliations in your literature search +## Using affiliations in your literature search **Affiliation filtering** The ADS interface enables you to refine your search using filters, located on the left hand side of the default view of search results. When you search for anything in the ADS, your search results also automatically populate all of the search filters which let you refine your results. There are several filters including: author, collection, keywords, and institutions. The Institutions filter is where you use the affiliation data to refine your searches. For example, if you search for "gravitational waves" and "year:2020" you'll get a list of over 3,300 papers published in the year 2020 that contain the phrase "gravitational waves". If you click *INSTITUTIONS* in the left column, you'll get an abbreviated list of the most-frequently seen affiliations among those 3,300 papers:
- +Screenshot of the ADS Institutions filter showing top affiliations for gravitational waves papers in 2020

If you select one of those affiliations (by checking the box to the left), you'll see the following:
- +Screenshot of the ADS Institutions filter showing limit to and exclude options after selecting Max Planck Institute

Note especially the "limit to" and "exclude" options; if you select "limit to", your original set of results will be refined to just those 155 papers having one or more coauthors from the Max Planck Institute:
- +Screenshot of ADS search results filtered to 155 papers with Max Planck Institute co-authors

@@ -87,12 +87,12 @@ If you do not see the results you expect, one or more of the following may help: -### Curated affiliation metadata: by the numbers +## Curated affiliation metadata: by the numbers We significantly expanded curated affiliation coverage in the ADS over the past twelve months. In January 2020, the ADS contained about 38.6 million individual author-affiliation pairs -- each affiliation of each author of all the papers, articles, and books in the ADS. Today, that number is about 42 million, an increase of 3.2 million (8%). Of those 42 million strings, 34.7 million (83%) have been matched to identifiers and can be searched via the affiliation filter. The remaining 7.3 million (17%) have not; they can be searched as a text field (i.e. with the "aff" keyword), but not via the *INSTITUTIONS* filter.
- +Chart showing 83% of ADS author-affiliation pairs matched to identifiers in 2021, up from 57% in 2020

@@ -100,13 +100,13 @@ This is a large improvement over last year's numbers, where only 22 million (57%
- +Chart showing the distribution of unmatched ADS affiliation strings, with 17% remaining unmatched in 2021

We streamlined the process of matching identifiers in 2020; matching strings to identifiers is still done by hand but we sped up the process by scripting aspects of the text manipulation and extraction process, searching for substrings common to different affiliation strings, and then using simple text processing and human analysis to confirm identifications. We placed particular emphasis on looking for substrings that appeared thousands of times, even if the individual affiliations containing those substrings may be less common. Many affiliations fell into this category, particularly individual universities represented in multiple categories in the ADS, such as physics, astronomy, chemistry, computer science and engineering. By targeting those substrings that occur most frequently, we can generate more matches overall, and we added them more quickly -- it was easier to disambiguate among departments and laboratories in a single university than across multiple institutions. This work is still in progress, and we are shifting focus to the country-level to ensure more complete international coverage. -### Improvements and additions over the past year +## Improvements and additions over the past year Another reason our coverage increased is that we expanded the number of identifiers to nearly 7000 different entities and parent-child relationships, which lets us match more institutions that are easily assignable, and helps us disambiguate entities that may have multiple parents or warrant better subdivision at the department or institution level. @@ -126,7 +126,7 @@ We have also added affiliation IDs for a partial list of Tribal Colleges and Uni There are comparatively few publications by authors affiliated with Tribal Colleges and Universities, and the papers written by TCU authors and coauthors in the ADS primarily focus on topics in Environmental Science and Science Education, which are not currently part of our core literature. Of those schools represented, Salish Kootenai College (Montana), Northwest Indian College (Pacific NW), Diné College (Arizona) and Fond du Lac Tribal College (Minnesota) have the most publications. TCUs may become more frequently represented if our scope widens to include more related sciences (e.g. planetary science and allied literature). We also want to ensure that their contributions are noted in existing literature, and that their contributions will be more easily tracked if researchers from these institutions increase their participation in the ADS core fields of astronomy and physics. -### Improving Affiliation Metadata: You Can Help! +## Improving Affiliation Metadata: You Can Help! Affiliation identification is an ongoing process and always will be. One of our tasks over the past year has been to fix errors in our affiliations metadata, including badly-parsed affiliations; we focused on papers having either the longest author list or the highest citations, but we know there are still some data that needs to be fixed. Likewise, there are many cases where an author has multiple affiliations and our representation is correct but can't be cleanly split into independent entities -- think of an author who lists "Departments of Chemistry and Physics, University of..." where we assigned IDs to both departments. We may identify such strings as one or the other, depending on which department we searched for first. In these cases, our ID is technically correct, but incomplete. diff --git a/_includes/_blogcontent/2021-08-04-openapi-docs.md b/_includes/_blogcontent/2021-08-04-openapi-docs.md index a9c703e4..b110f4bf 100644 --- a/_includes/_blogcontent/2021-08-04-openapi-docs.md +++ b/_includes/_blogcontent/2021-08-04-openapi-docs.md @@ -8,7 +8,7 @@ However, while our existing API documentation covered the most widely used featu The OpenAPI spec is a language-agnostic, widely adopted industry standard for documenting APIs in a machine-readable way. We spent weeks documenting and describing 80+ user-facing (and, for internal use, 70+ data pipeline and internal) API operations, resulting in a comprehensive document that combines descriptions, examples, and schema for each operation. This document is now available to explore visually using our new [beautiful, easy to use documentation](../../help/api/api-docs.html)[2](#footnote1).
- + Screenshot of the ADS OpenAPI documentation interface showing the list of API operations New API help documentation

@@ -18,7 +18,7 @@ Our [new API documentation](../../help/api/api-docs.html) looks a little overwhe This is all very useful already, if similar to the existing Jupyter notebook documentation. Where these docs really shine, though, are with the built-in try-me functionality. To use this, first [get your API key](https://ui.adsabs.harvard.edu/user/settings/token) and copy it into the box in the [Authentication section](../../help/api/api-docs.html#auth) and click Set. Now you can try out the API directly from this documentation! Let’s look at an example.
- + Screenshot of the API token authentication input box in the ADS API documentation API token authentication box

@@ -26,7 +26,7 @@ This is all very useful already, if similar to the existing Jupyter notebook doc We’ll start with a basic search, using the operation labeled [Search ADS](../../help/api/api-docs.html#get-/search/query). This operation uses the GET method and the endpoint `/search/query`. A longer description, with examples, is also provided in the documentation.
- + Screenshot of the Search ADS operation in the API documentation showing the GET /search/query endpoint Search ADS operation

@@ -38,7 +38,7 @@ Some other things to note about the request parameters section: * Below some of the parameters, there’s an example shown; click on the example to fill it in. You can also use the “fill example” button at the bottom of the list of parameters to fill all available examples.
- + Screenshot of the Search ADS request parameters panel with q and fl fields filled in Search ADS request parameters

@@ -46,7 +46,7 @@ Some other things to note about the request parameters section: Once you’ve filled in the parameters you’d like, scroll to the end of the parameter list and click Try. This will format your request, send it, and return the results. The request response is shown in the “Response” tab, in JSON format. The “responseHeader” section contains some information about the request, while the “response” section (shown below) contains the actual request results. In this example, 556,985 total results were found, and the page is displaying the first 10 in the Response box.
- + Screenshot of the Search ADS API response showing JSON results with bibcode and title fields Search ADS response

@@ -54,7 +54,7 @@ Once you’ve filled in the parameters you’d like, scroll to the end of the pa You can scroll through the search results here, or you can click on the “curl” tab to copy the request formatted using your input parameters to use in your own scripts.
- + Screenshot of the curl tab in the Search ADS documentation showing a copyable curl command Search ADS curl command: copy this into your terminal to run the query as formatted

@@ -62,7 +62,7 @@ You can scroll through the search results here, or you can click on the “curl This works similarly for operations that have the POST HTTP request method, but there is a slight difference. Let’s look at one more example. The [BibTeX export for multiple bibcodes](../../help/api/api-docs.html#post-/export/bibtex) uses the POST method. You can see that while this operation doesn’t have any parameters (though some POST operations do), it does have a request body, which is used to pass in the bibcodes you want to export. The default view for a request body is the “schema” tab, which shows the information you can pass in via the body (again, the fields marked with an asterisk are required).
- + Screenshot of the BibTeX export POST operation in the API documentation showing the request body schema BibTeX export for multiple bibcodes

@@ -70,7 +70,7 @@ This works similarly for operations that have the POST HTTP request method, but To test this operation, click on the “example” tab. It defaults to an empty box; click on “fill example” to fill in the placeholder text that demonstrates the proper formatting.
- + Screenshot of the BibTeX export Example tab showing the request body with placeholder bibcodes Request body; click on the Example tab, then "fill example" to show the proper request body formatting

@@ -78,7 +78,7 @@ To test this operation, click on the “example” tab. It defaults to an empty Fill in your bibcodes in the placeholder text:
- + Screenshot of the BibTeX export request body with user-entered bibcodes replacing the placeholder text Edit the placeholder request body as necessary

diff --git a/_includes/_blogcontent/2021-11-12-arc-ssad-project.md b/_includes/_blogcontent/2021-11-12-arc-ssad-project.md index 246bc469..41eedb52 100644 --- a/_includes/_blogcontent/2021-11-12-arc-ssad-project.md +++ b/_includes/_blogcontent/2021-11-12-arc-ssad-project.md @@ -7,7 +7,7 @@ As a recent addition to the ADS Team supporting curation efforts and assisting i In this blog post I will outline the goals I established, the steps I took to accomplish them, and lessons learned. To accomplish this project, I used a combination of my own knowledge and expertise, read API documentation, searched online for solutions as needed, and collaborated with team members to debug and learn the ins and outs of the ADS API. -### Project Outline and Goals +## Project Outline and Goals The source data used in this project was an Excel spreadsheet provided of ARC/SSAD’s bibliographic holdings (with metadata for authors, 'org code' as a unique identifier of NASA's organizational structure, title, journal information, and DOI if available), which was split up into three sheets by Branch (Astrophysics Branch, the Planetary Systems Branch, and the Exobiology Branch). The data provided was obtained from NASA's Astrobiology Habitable Environments Database (AHED). diff --git a/_includes/_blogcontent/2022-09-06-ads-object-search.md b/_includes/_blogcontent/2022-09-06-ads-object-search.md index a44a64e5..918ea673 100644 --- a/_includes/_blogcontent/2022-09-06-ads-object-search.md +++ b/_includes/_blogcontent/2022-09-06-ads-object-search.md @@ -1,18 +1,16 @@ Searching for publications that mention, in some way, a specific astronomical object is one of the common use cases of the ADS. This blog aims to illustrate some of the caveats associated with these types of queries and provide some pointers. -If a publication mentions an astronomical object in its title or abstract, this object probably plays a significant role in this publication. If the object only appears in the body of the paper, the object most likely appears as part of a catalog or in a less prominent role. If your goal is, for example, to find publications that focus on the star Aldebaran, you search for mentions in basic metadata (title, keywords or abstract). This is precisely the function of the so-called "unfielded query" in the ADS. Unfielded queries, without query fields[^1], will search the basic metadata of the publications (author, publication year, title, abstract, keywords). In the case of our example, focusing on publications in the astronomy collection, this query is +If a publication mentions an astronomical object in its title or abstract, this object probably plays a significant role in this publication. If the object only appears in the body of the paper, the object most likely appears as part of a catalog or in a less prominent role. If your goal is, for example, to find publications that focus on the star Aldebaran, you search for mentions in basic metadata (title, keywords or abstract). This is precisely the function of the so-called "unfielded query" in the ADS. Unfielded queries, without query fields (a query field in general has the format of a field name directly followed by a colon, like `author:`; see [this page](https://ui.adsabs.harvard.edu/help/search/comprehensive-solr-term-list) for a full list), will search the basic metadata of the publications (author, publication year, title, abstract, keywords). In the case of our example, focusing on publications in the astronomy collection, this query is ``` Aldebaran collection:astronomy ``` -[^1]:A query field in general has the format of a field name, directly followed by a colon (like e.g. `author:`). The result of a fielded query is that only specific data types in our database are queried with the data provided (see [this page](https://ui.adsabs.harvard.edu/help/search/comprehensive-solr-term-list) in our online Help for a comprehensive list of query fields) - Before going into specifics of search technicalities, let's first explore the question of the necessity of adding the collection filter (restricting the query to the ADS Astronomy collection). The ADS holdings cover a wide range of disciplines; this is the result of indexing multidisciplinary publications like Science, Nature and arXiv e-prints, but also because we include the literature that is cited by and which cites the core literature. This is an important fact to keep in mind when exploring the ADS holdings. Often, names of astronomical and planetary objects are taken from areas like mythology. It also happens that, for example, projects, services or companies, unrelated to astronomy, are named after astronomical objects (like Aldebaran Robotics). Records not fetched by the query above are retrieved by the query ```Aldebaran NOT collection:astronomy```. Inspection of the results show publications that are definitely related to the star Aldebaran. As illustrated in the screenshot (Figure 1), it helps to check the highlights for the context of the matches. For example, the arXiv record [The Ancient Astronomy of Easter Island: Aldebaran and the Pleiades](https://ui.adsabs.harvard.edu/abs/2016arXiv161008966R/abstract) (in the arXiv category `Physics - History and Philosophy of Physics`) and the SPIE record [Measurement of the speed of light from extraterrestrial sources](https://ui.adsabs.harvard.edu/abs/2015SPIE.9608E..0EW/abstract) appear to be related to the star Aldebaran. There are also records that are obviously unrelated to the star (e.g. humanoid robots, Aldebaran Sandstone). In the ADS curation workflow we attempt to classify records from multidisciplinary sources (like the journals Science and Nature). In some cases it may be better to optimize your query beforehand (by adding filters), while in other cases it will be better to cast a wide net first and apply filters afterwards. The best strategy depends on one's goals.
- + Screenshot of ADS search results for Aldebaran query with highlights enabled showing matching contexts Figure 1: Results of the query for Aldebaran, with highlights turned on

@@ -42,7 +40,7 @@ that will cause the ADS search engine to make use of these correspondences provi What happens when the `object:` query field is used? Since we cannot assume that a user will specify canonical object names in their queries, we need to make sure that the object names provided are translated into their canonical equivalents. This is because SIMBAD and NED provide us correspondences between publications and canonical names of objects. Both SIMBAD and NED provide a translation service. Having established these canonical equivalents, the ADS search engine is able to find all associated publications, according to the Boolean relationship specified. Additionally, the object names (as specified in the query) are also used in an ADS query against abstracts, titles and keywords in the astronomy collection (with synonym replacement switched off). The result set is a combination of all these matches. Object queries that target just one service (e.g. SIMBAD) are not currently supported.
- + Screenshot of the ADS Classic Form showing the Object search field for object-based queries Figure 2

diff --git a/_includes/_blogcontent/2022-12-29-uat-integration.md b/_includes/_blogcontent/2022-12-29-uat-integration.md index f23fbf34..9040e337 100644 --- a/_includes/_blogcontent/2022-12-29-uat-integration.md +++ b/_includes/_blogcontent/2022-12-29-uat-integration.md @@ -31,12 +31,11 @@ As ADS adopts use of the UAT across its astronomy collection, we encourage all a While the AAS has assumed formal ownership of the UAT, the thesaurus remains available under a Creative Commons License, ensuring its widest use while protecting the intellectual property of its contributors. Development and maintenance are stewarded by a broad group of parties with a direct stake in the UAT; this includes professional associations (IVOA, IAU), learned societies (AAS, RAS), publishers (IOP, AIP), software developers, librarians, and other curators working for major astronomy institutes and data archives. -The UAT has been implemented by an increasing number of journals, research organizations, and systems[^1]. - -[^1]: Current adoptees include: - - American Astronomical Society journals, including The Astronomical Journal (AJ), The Astrophysical Journal (ApJ), ApJS, ApJL, The Planetary Science Journal (PSJ), and Research Notes of the AAS (RNAAS) - - Astrophysics Data System (ADS) - - Publications of the Astronomical Society of the Pacific (PASP) - - International Virtual Observatory Alliance (IVOA) - - Space Telescope Science Institute (STScI) for the Hubble Space Telescope (HST) and James Webb Space Telescope (JWST) proposal systems - - Icarus - in formulation for 2023 +The UAT has been implemented by an increasing number of journals, research organizations, and systems. Current adoptees include: + +- American Astronomical Society journals, including The Astronomical Journal (AJ), The Astrophysical Journal (ApJ), ApJS, ApJL, The Planetary Science Journal (PSJ), and Research Notes of the AAS (RNAAS) +- Astrophysics Data System (ADS) +- Publications of the Astronomical Society of the Pacific (PASP) +- International Virtual Observatory Alliance (IVOA) +- Space Telescope Science Institute (STScI) for the Hubble Space Telescope (HST) and James Webb Space Telescope (JWST) proposal systems +- Icarus - in formulation for 2023 diff --git a/_includes/_blogcontent/2023-03-20-curation-model.md b/_includes/_blogcontent/2023-03-20-curation-model.md index 9354dd54..0443a18b 100644 --- a/_includes/_blogcontent/2023-03-20-curation-model.md +++ b/_includes/_blogcontent/2023-03-20-curation-model.md @@ -7,7 +7,7 @@ The basic intellectual structure of the ADS can be described using a bullseye mo * Planetary Science
- + Bullseye diagram showing ADS tiered curation model with Core Collection at center surrounded by Inner and Outer Rings
Figure 1: ADS's tiered curation model. The core collection represents disciplines where its curation is strongest and its coverage is authoritative. The surrounding tiers are connected to the core via the citation network. @@ -41,7 +41,7 @@ In the following step, the librarian walks over to the shelf with the journal vo There are some compelling reasons to favor the Eigenfactor. Some of them are the fact that it weights citations with the importance of the citing journals, the fact that it exploits the entire citation network and ignores self-citations and that it has a solid mathematical underpinning and an intuitive stochastic interpretation. Another reason for favoring the Eigenfactor is the fact that it uses a 5-year window to gather citations. This allows, in general, a broader evaluation of journal citations, in particular for disciplines with longer citing half lives.
- + Directed network diagram showing citation relationships between journals as nodes and edges Figure 2: Directed network based on citation relationship between journals. The nodes represent journals. This is a fictitious network, for illustration purposes only.
@@ -52,7 +52,7 @@ At its core, the algorithm that calculates the Eigenfactor values is the well-kn The results are shown in figure 3. The fact that values are not equal is no surprise, because the citation networks in the ADS and Web of Science are different. The encouraging result is that the values have a very strong correlation.
- + Scatter plot comparing journal Eigenfactor values calculated from ADS citation data versus JCR values Figure 3: Comparison between Eigenfactors calculated from ADS data and provided in the JCR. The categorization is based on journal assignments provided in the JCR.
diff --git a/_includes/_blogcontent/2023-04-19-scix.md b/_includes/_blogcontent/2023-04-19-scix.md index a3288a85..090843d9 100644 --- a/_includes/_blogcontent/2023-04-19-scix.md +++ b/_includes/_blogcontent/2023-04-19-scix.md @@ -13,7 +13,7 @@ Having an open, sophisticated digital library has had an enormous impact on astr
- + Bar chart comparing ADS acknowledgements in astronomy literature to HST and Chandra telescope acknowledgements over time
Figure 1. Acknowledgments found in the scholarly literature to ADS, and NASA’s most prominent astrophysics missions: the Hubble Space Telescope (HST), and the Chandra X-ray Telescope. HST and Chandra numbers include required acknowledgments of research grant funding. diff --git a/_includes/_blogcontent/2023-10-23-ads-models-and-datasets.md b/_includes/_blogcontent/2023-10-23-ads-models-and-datasets.md index 91d8848e..18d00c2d 100644 --- a/_includes/_blogcontent/2023-10-23-ads-models-and-datasets.md +++ b/_includes/_blogcontent/2023-10-23-ads-models-and-datasets.md @@ -1,10 +1,10 @@ -### Introduction +## Introduction The Astrophysics Data System (ADS) has been developing Natural Language Processing tools and datasets to further enhance its data holdings and services. As part of this effort, we have been building and curating datasets to train deep learning models. These new tools, and more that will build upon them, will both provide a richer user experience and allow internal processes to be scaled-up. Further, we expect that these tools will be useful to researchers in a variety of fields. This post will describe our models and datasets for interested researchers. We are strong proponents of open science, and we endeavor to make our datasets publicly available and easy to access. This post contains links to our curated datasets and will be updated as more datasets are created. The models are licensed under an [MIT license](https://opensource.org/license/mit/) and the datasets are licensed under a [CC-BY 4.0 license](https://creativecommons.org/licenses/by/4.0/). Briefly, these licenses allow researchers to use, share, modify or build upon these works as long as appropriate attribution is given. If there are any questions about fair usage, contact us at [ADS help](mailto:adshelp@cfa.harvard.edu). -### astroBERT +## astroBERT To support broad community participation in these efforts, we have recently released the [astroBERT](https://huggingface.co/adsabs/astroBERT) astrophysics-specific language model. A language model is a statistical representation of the relationships among words, and even sub-word units called tokens, in a corpus of text. By creating a model that is astronomy specific, we can better account for the nuances of the language used in the astrophysical literature. @@ -19,14 +19,14 @@ astroBERT was trained using [Masked Language Model](https://huggingface.co/docs/ Further technical details about astroBERT can be found in the following [paper](https://arxiv.org/abs/2112.00590). The astroBERT page on Hugging Face includes documentation about how to access and utilize the model, as well as all publicly available versions. -### Detecting Entities in the Astrophysical Literature (DEAL) +## Detecting Entities in the Astrophysical Literature (DEAL) The [Detecting Entities in the Astrophysical Literature](https://huggingface.co/datasets/adsabs/WIESP2022-NER) (DEAL) dataset is a curated dataset for Named Entity Recognition. This task involves identifying predetermined entities in text, such as Organization or Location. The dataset consists of text fragments obtained from the astrophysical literature. The journals that the text fragments were obtained from are the Astrophysical Journal, Astronomy & Astrophysics, and the Monthly Notices of the Royal Astronomical Society. All text fragments are from recent publications, between the years of 2015 and 2021. Each text fragment is roughly a paragraph in length, and originates from one of two parts of an article. The first are fragments from the fulltext, consisting of all sections of the body of the article, excluding the abstract and acknowledgments sections. The second are fragments from the acknowledgments section of the article. Roughly 6000 text snippets were labeled, containing over 147,000 labeled entities. Figure 1 shows an example of a manually labeled text snippet.
- + Example of a manually labeled astrophysical text snippet with named entity tags from the DEAL dataset
Figure 1: Example of a manually labeled full text snippet. @@ -37,7 +37,7 @@ Thirty-three different entities, composed of general and astrophysical entities,
- + Bar chart showing counts of labeled entity categories in the DEAL dataset, split by fulltext (blue) and acknowledgments (red)
Figure 2: Counts of labeled entities. Red denotes entities labeled in the Acknowledgments section of a paper, and blue denotes entities labeled in the body of a paper. @@ -49,7 +49,7 @@ Thirty-three different entities, composed of general and astrophysical entities, The DEAL dataset was used as part of a shared task in the [First Workshop on Information Extraction from the Scientific Literature](https://ui.adsabs.harvard.edu/WIESP/2022/) (WIESP 2022) as part of the AACL-IJCNLP 2022 conference. The proceedings of this workshop are part of the [ACL Anthology](https://aclanthology.org/volumes/2022.wiesp-1/). -### Function Of Citation in Astrophysics Literature (FOCAL) +## Function Of Citation in Astrophysics Literature (FOCAL) The [Function Of Citation in Astrophysics Literature](https://huggingface.co/datasets/adsabs/FOCAL) (FOCAL) dataset is a curated dataset for citation context analysis. Citation context analysis “facilitates the syntactic and semantic analysis of the contents of the citation context to understand how and why authors discuss others research work” ([Kunnath et al. 2021](https://direct.mit.edu/qss/article/2/4/1170/107610/A-meta-analysis-of-semantic-classification-of)). Citation context analysis includes the determination of citation function, or the reason an author is including a particular citation; citation polarity, or the author’s sentiment towards the cited work, either positive or negative; and citation impact, or the importance of a cited work to the citing work. @@ -86,7 +86,7 @@ We are considering a set of eight potential citation functions. These are: The snippets that contain the citations are obtained from over 25,000 astronomy articles, from the same journals and publication years as the DEAL dataset. From this set of articles, over 2 million citations and their context are harvested. Further, only citations with context sizes between 2,000 and 10,000 characters are selected. This is to allow the determination of what portions of the context are most relevant to understanding the citation’s function. A domain area expert manually examined these text snippets to determine the citation function as well as label the relevant context. In total there are 6023 instances of annotated citations. Table 1 shows the number of instances for each citation function category.
- + Example of a manually labeled citation context text snippet from the FOCAL dataset showing multiple citation functions
Figure 3: An example of a manually labeled citation context text snippet. @@ -99,13 +99,13 @@ There are a number of open questions in citation context analysis research that The FOCAL dataset will be used for the [Second Workshop on Information Extraction from the Scientific Literature](https://ui.adsabs.harvard.edu/WIESP/2023/shared_task_1) (WIESP 2023) part of [IJCNLP-AACL 2023](http://www.ijcnlp-aacl2023.org/). -### We Want to Hear From You +## We Want to Hear From You If you find any of these datasets useful in your research or if you are working on similar efforts, we would like to hear from you. You can contact the ADS Team at [ADS help](mailto:adshelp@cfa.harvard.edu). -### Linked Resources +## Linked Resources astroBERT model: [https://huggingface.co/adsabs/astroBERT](https://huggingface.co/adsabs/astroBERT) diff --git a/_includes/_blogcontent/2024-01-03-aas-2024.md b/_includes/_blogcontent/2024-01-03-aas-2024.md index 88203c36..328444d0 100644 --- a/_includes/_blogcontent/2024-01-03-aas-2024.md +++ b/_includes/_blogcontent/2024-01-03-aas-2024.md @@ -1,4 +1,4 @@ - +Banner for the 243rd American Astronomical Society Meeting in New Orleans, January 2024 Join us at the [243rd American Astronomical Society (AAS) Meeting](https://aas.org/meetings/aas243) from 7-11 January 2024 in New Orleans, LA for an insightful exploration of the [Science Explorer (SciX)](https://www.scixplorer.org/) and the implications of its recent launch for the ADS user community. diff --git a/_includes/_blogcontent/2024-02-26-userfeedback-2024.md b/_includes/_blogcontent/2024-02-26-userfeedback-2024.md index d894d79c..7125b31a 100644 --- a/_includes/_blogcontent/2024-02-26-userfeedback-2024.md +++ b/_includes/_blogcontent/2024-02-26-userfeedback-2024.md @@ -2,11 +2,11 @@ The virtual gathering of the [Astrophysics Data System Users Group (ADSUG)](../a The ADSUG meeting delved into these user insights, providing a collaborative space for discussions on maximizing the scientific productivity of the community we serve. The [meeting's agenda](../about/adsug/past_meetings/2023-11-16-202311-program.html) included recommendations for changes and improvements to services and procedures, reflecting the ADSUG's advisory role. -### User Survey: Illuminating Current ADS Strengths & User Aspirations for SciX +## User Survey: Illuminating Current ADS Strengths & User Aspirations for SciX The survey underscored the significance of ADS in the astrophysics community, with 91.4% of survey respondents reporting daily or weekly use of the system and 95.52% indicating they were either highly likely or likely to recommend the use of ADS to others. A high volume of use and high promoter scores (10 being the highest) were typically reported together. The survey was advertised on the ADS website, through social media, and distributed though newsletters and other online community forums relevant to the SciX expansion. Notably, 56.7% of responses came from existing ADS users who found the survey through a link on the ADS website homepage.
- + Charts showing ADS users with high usage frequency are also highly likely to recommend ADS to others Figures 1-3: ADS users who reported a high volume of use were also likely to be highly likely or likely to recommend the use of ADS to others.
@@ -17,7 +17,7 @@ Users praised ADS for its role as a unified hub, seamlessly integrating publishe Users are eager for enhancements across various aspects of the ADS platform, with a notable interest in improved search functionality. They seek additional search capabilities, like searching by specific criteria such as author name placement, paper length, or details related to astronomical objects, to make searching more efficient and targeted.
- + Charts showing percentage of survey responses requesting improvements to ADS components and highly valued features
Figures 4 & 5: % of user survey responses requesting improvements or innovations to different ADS components as well as the % of responses citing specific features as highly valuable features of ADS. @@ -39,19 +39,19 @@ Integration and external links also present opportunities for improvement, with The survey results also highlighted a collective eagerness of ADS users to explore new scientific territories. Users desire interdisciplinary connections, with a focus on mathematical and statistical content, chemistry, astrobiology, physics, and other fields beyond the traditional scope of astrophysics. The ADSUG meeting served as a platform for delving deeper into these aspirations as well as the many diverse suggestions submitted by users to enhance the portal’s existing capabilities.
- + Chart showing percentage of survey responses requesting expansion of ADS and SciX to additional subject areas
Figure 6: % of user survey responses requesting expansion of ADS & SciX to include additional content in these subject areas.

-### Addressing User Concerns +## Addressing User Concerns While users expressed their hopes for SciX, they also shared concerns about potential challenges during the transition. The ADS team, as outlined in discussions during the ADSUG meeting, committed to a transparent and collaborative approach. We will maintain existing functionalities, ensuring a seamless transition for users. Discussions during the meeting revolved around strategies to address user concerns and maintain a user-centric approach throughout the transition process. Specific questions from users, raised in the survey, became focal points of discussion at the ADSUG meeting. Participants scrutinized topics such as changes to the ADS application programming interface (API), alterations to search functionality, and the potential dilution of search results, emphasizing the collaborative efforts between the ADS team and the user community to navigate the forthcoming changes successfully. Attendees also discussed the ongoing importance of communication and thorough outreach efforts. -### Conference Outreach & Engagement +## Conference Outreach & Engagement In response to the ADUG's emphasis on outreach, the ADS team initiated outreach interactions with both established and new users during the [American Geophysical Union Fall Meeting](../scixblog/AGUSciXLaunch) and the [American Astrophysical Society Meetings #243](../scixblog/aas-2024). These conferences provided valuable opportunities for us to connect with the broader scientific community, offering insights and perspectives that further inform the SciX transition. The bullet points below encapsulate direct responses to the inquiries raised by the community during the ADS team’s conference interactions. @@ -65,5 +65,5 @@ The bullet points below encapsulate direct responses to the inquiries raised by * **Expanded Staff Expertise:** The ADS team acknowledges the need for added expertise as we transition into SciX, because we remain dedicated to supporting users effectively. * **User Feedback:** The ongoing [call for user feedback](../feedback/general?from=%2F) ensures that SciX remains attuned to the diverse needs of the scientific community, including astronomers. -### Conclusion: A Collaborative Transition +## Conclusion: A Collaborative Transition In conclusion, the shift from ADS to SciX is a collaborative effort between the ADS team and our user community. Shaped by survey insights, ADSUG discussions, conference engagements, and your comments, the SciX team’s user-centric development works to ensure it meets community needs. SciX aims to preserve ADS strengths while pioneering new avenues for science discovery. As the ADS/SciX team looks ahead, your input remains key in shaping the future of SciX. Share your thoughts, insights, and suggestions at [help@scixplorer.org](mailto:help@scixplorer.org). diff --git a/_includes/_blogcontent/2024-03-06-introducing-scix-ambassador-program.md b/_includes/_blogcontent/2024-03-06-introducing-scix-ambassador-program.md index ed9d5f51..13b879f8 100644 --- a/_includes/_blogcontent/2024-03-06-introducing-scix-ambassador-program.md +++ b/_includes/_blogcontent/2024-03-06-introducing-scix-ambassador-program.md @@ -1,9 +1,9 @@ -### Introducing the Science Explorer Ambassador Program +## Introducing the Science Explorer Ambassador Program The [Science Explorer (SciX)](https://scixplorer.org) team is thrilled to announce the launch of the SciX Ambassador Program! This initiative marks a new chapter in the evolution of the Astrophysics Data System (ADS) into SciX, with a significant leap in promoting interdisciplinary communication and research. To further this mission, we are seeking approximately 12 researchers to become our Lead Ambassadors, representing diverse disciplines across NASA, including Astrophysics, Planetary Science, Earth Science, Heliophysics, and Biological & Physical Sciences. Our goal is to drive forward the vision of interdisciplinary engagement and innovation as a cornerstone of SciX.
- + SciX Ambassador Program promotional flyer with program details and application information
SciX Ambassador Program Flyer @@ -22,7 +22,7 @@ The Lead Ambassadors will serve a two-year term, during which they will particip The SciX Ambassador Program aims to empower ambassadors to effectively promote the platform, improve it through community feedback, gain visibility and recognition for their work, and build a robust online community that connects researchers from diverse fields. Through their efforts, the ambassadors will play a pivotal role in advancing the mission of interdisciplinary research and open science. -### Key Program Highlights +## Key Program Highlights - **Presentations:** Ambassadors will present on SciX twice a year in various formats, such as locally at their institute, virtually at a meeting, or in person at a workshop. - **Workshop:** A 2.5-day workshop at the [Center for Astrophysics \| Harvard & Smithsonian](https://www.cfa.harvard.edu/) (August 21 - 23, 2024), where ambassadors will connect with the SciX team, learn community engagement skills, and receive training on the SciX platform. diff --git a/_includes/_blogcontent/2024-06-04-HistoricLit.md b/_includes/_blogcontent/2024-06-04-HistoricLit.md index aa0069ac..abdfe799 100644 --- a/_includes/_blogcontent/2024-06-04-HistoricLit.md +++ b/_includes/_blogcontent/2024-06-04-HistoricLit.md @@ -1,5 +1,5 @@
- + Animated display of historic observatory publication title pages available in SciX
Historic Observatory Publications diff --git a/_includes/_blogcontent/2024-06-13-data-linking-I.md b/_includes/_blogcontent/2024-06-13-data-linking-I.md index d2e6b719..94440ff9 100644 --- a/_includes/_blogcontent/2024-06-13-data-linking-I.md +++ b/_includes/_blogcontent/2024-06-13-data-linking-I.md @@ -1,7 +1,7 @@ One of the distinguishing features of the Science Explorer (SciX) is its integration of literature with research data, software, and services. SciX records accrue links to related research objects through curated text mining (finding citations and links to data and software in the publisher manuscript) and metadata enrichment (aggregating bibliographies maintained by missions and archives). Our work with community-led initiatives such as the [Asclepias](https://ui.adsabs.harvard.edu/blog/asclepias) project and the [Astrophysics Source Code Library](https://ascl.net/) have put ADS at the forefront of the FAIR efforts in the physical sciences. SciX extends these efforts to the remaining NASA Science disciplines.
- + Graph diagram of SciX holdings showing nodes for articles, data, and software connected by colored relationship arrows
Figure 1. The SciX holdings represented as a graph. The different shapes represent different resources (articles, data, software) and the different colored arrows represent relationships (like cites, supplements,...). Some of these links, like "record A cites record B" (e.g. the black arrows) only have meaning within SciX, because it is a relationship between two entities that only exist within SciX.
@@ -15,7 +15,7 @@ The holdings of SciX can be represented as a graph, illustrated by figure 1. The By construction links can, in principle, point to a resource outside of SciX, with the exception of two relationships that represent the following: "citations" and "co-readership", both of which are only meaningful within SciX context. With this relation both the source and the target must correspond with nodes that lie within the circle in figure 1. The nodes within the circle represent what is indexed in SciX; these are actual, searchable database records, and their metrics (such as citations and reads) are tracked by SciX. Linked resources are not searchable, but they can provide a means for filtering search results. As an example, software packages cited in the literature are indexed records, which means you can use a SciX search to find all packages written by a particular researcher or cited more than N times. On the other hand, data products hosted by NASA archives are linked resources. While you can’t discover them with a search, you can find all the SciX records which link to one or more data products hosted by a particular archive such as MAST, Chandra, or SIMBAD. Table 1 summarizes the differences between indexed and linked information in SciX.
- + Table comparing indexed versus linked information in SciX, highlighting key differences in discoverability and metrics
Table 1: Highlights of differences between what is indexed versus what is linked to in SciX. @@ -25,7 +25,7 @@ By construction links can, in principle, point to a resource outside of SciX, wi The SciX curation team receives digital assets (metadata, fulltext, relational data) from a range of sources and in a great variety of formats (ranging from simple ASCII text to highly structured XML data). These sources consist of collaborators (publishers, repositories, societies), users (missing publications, corrections, associations), other sources (mostly Crossref and DataCite) and SciX itself (even though internal, curated records are still a form of data supply, from a workflow perspective). These assets contain information that, down the line, need to become discoverable through the SciX user interface; to make this possible, we need an intricate process of extracting all the necessary elements from the original assets and putting them into a form that can be processed further. This workflow is made possible by format-specific parsers and the SciX [ingest data model](https://github.com/adsabs/ingest_data_model). Since data is often not perfectly formatted, the curation process in the ETL layer needs to be able to deal with all kinds of issues.
- + Diagram of the SciX data ingestion pipeline showing ETL, augmentation, import, and indexing layers
The augmentation layer enriches the original data with all kinds of information. In addition to making publications discoverable, SciX also maintains a citation graph. This graph is the result of the reference matching software in the augmentation layer; this framework takes reference data, either supplied or extracted, and attempts to match these to existing SciX records. The affiliation pipeline normalizes affiliations into canonical formats (see [this blog](https://ui.adsabs.harvard.edu/blog/affils-update)). The mining of data links will be discussed in part II of this series. The software citation capture was discussed in [this blog](https://ui.adsabs.harvard.edu/blog/asclepias). The preprint matching process (called "docmatching") is highlighted in [this blog](https://ui.adsabs.harvard.edu/blog/docmatcher). We are developing a process that tags publications with planetary feature names, taken from the USGS Gazetteer of Planetary Nomenclature (see [this publication](https://scixplorer.org/abs/2023arXiv231208579S/abstract)). Future augmentations will include a pipeline that will assign publications to one of the disciplines represented in SciX (document classifier) and a pipeline that will assign terms from the Unified Astronomy Thesaurus (UAT tagger), whenever possible. diff --git a/_includes/_blogcontent/2024-07-01-data-linking-II.md b/_includes/_blogcontent/2024-07-01-data-linking-II.md index b06e5fdf..e2bf5f8f 100644 --- a/_includes/_blogcontent/2024-07-01-data-linking-II.md +++ b/_includes/_blogcontent/2024-07-01-data-linking-II.md @@ -1,7 +1,7 @@ # Introduction
- + Diagram illustrating the Research Life Cycle and the role of SciX in connecting research artifacts

@@ -17,7 +17,7 @@ Since the whole of the artifacts referenced by a scholarly article forms the bes Citations are just one form of the linkages we are referring to. Linkages are essentially so-called semantic triples (figure 2): a triple is a sequence of three entities that codifies a statement about semantic data in the form of subject–predicate–object expressions.
- + Diagram showing a semantic triple structure with subject, predicate, and object nodes representing data linkages

@@ -25,7 +25,7 @@ Citations are just one form of the linkages we are referring to. Linkages are es The predicate describes the relationship between two entities, one the subject and the other the object. The relationship within the framework of SciX can be one of two: *cites* or *mentions*. Also, within this framework, the subject always refers to a publication and currently the object refers to either a data product or software. At this point it is good to explain the difference between the treatment of these two relationships within the SciX context, in particular the consequences. Table 1 summarizes the difference between the two scenarios in SciX. The row "Form" corresponds to another limitation within SciX: only objects that have a URL associated with them can be considered; objects without URL are per definition not actionable.
- + Table comparing data mentions versus data citations in SciX, covering form, action, and consequences
Table 1: Difference between mentions and citations. In the case of cites, only DOIs are in principle actionable because they have harvestable metadata associated with them. Cites with other identifiers are actionable if the cited work is already indexed. @@ -39,7 +39,7 @@ In this blog, we focus on the cases where the object is a data product. In the n One of the distinguishing features of SciX is the presence of links from its records to research archives and databases. This is particularly significant for the core astronomy journals which work with archive curators to create and maintain rich online resources associated with the articles they publish. As an example, 70% of articles published in the main astronomy journals during 2023 have links to data products. Historically, the links have been created by curators upon the ingestion of datasets published with the article (as is the case for [VizieR data tables](https://scixplorer.org/search?q=bibstem%3AyCat&sort=score+desc%2Cdate+desc&p=1)), cross-referencing of astronomical object measurements (SIMBAD and NED), or telescope bibliographies (Astrophysics Data Archives such as Chandra, MAST, IRSA, HEASARC, etc). The ADS, and now SciX, has been working with collaborators at these institutions to enable links between its records and these datasets on a regular basis, allowing for the curated links to be exposed to the end user.
- + Screenshot of a SciX abstract page showing data links section with labeled links to external archives

@@ -65,7 +65,7 @@ The *Author* facet will show you the most prolific authors associated with these To get some insight into the science topics covered by these publications we generate the [Paper Network](https://scixplorer.org/search/paper_network?q=NICMOS+property%3A%28data+refereed+openaccess%29+&sort=score+desc%2Cdate+desc&p=1). By default, this network is generated for the first 400 publications; some additional details can be generated by increasing this amount (with a maximum of 1,000) and regenerating this network diagram. Figure 4 (left) shows the results.
- + Two paper network diagrams for NICMOS publications, showing topic clusters at different levels of granularity

@@ -80,7 +80,7 @@ In a similar way we can explore the use of data links from a specific data repos Just like before, the Paper Network can be used to indicate the range of topics discussed in the publications returned by the query. Figure 5 shows the results for data hosted at NOAA (left) and data hosted at the Oak Ridge National Laboratory Distributed Active Archive Center, as an additional example (right).
- + Two paper network diagrams showing science topics for publications with data hosted at NOAA and Oak Ridge DAAC

@@ -92,7 +92,7 @@ The next example is to illustrate how to find publications that may be able to p The results are shown in figure 6. The diagram on the left shows the results for the initial query and the diagram on the right shows the results when we generate the paper network for the publications in the orange segment only.
- + Two paper network diagrams showing topic clusters for exoplanet atmosphere publications with open access data links

diff --git a/_includes/_blogcontent/2024-08-01-data-linking-III.md b/_includes/_blogcontent/2024-08-01-data-linking-III.md index 36778eff..845a23f4 100644 --- a/_includes/_blogcontent/2024-08-01-data-linking-III.md +++ b/_includes/_blogcontent/2024-08-01-data-linking-III.md @@ -3,7 +3,7 @@ This blog is the final part in the series on data linking and indexing in the [Science Explorer](https://scixplorer.org/) (SciX). In the [first](https://scixplorer.org/scixblog/data-linking-I) part we provided a general overview of the holdings in SciX, and the [second](https://scixplorer.org/scixblog/data-linking-II) part discussed the role and merits of linked data in this service. In this part we do something similar for cited data products. There is no fundamental difference between articles citing other articles (something which we have been recording for decades) and articles citing data; actually, the "cites" relationship can be between any bibliographic asset. Citations are just one small subset of the entire graph of linkages between research assets; if we add the constraint that all these research assets must have a persistent identifier (PID), this graph is also referred to as the PID graph. A citation graph is a special case of a PID graph. Figure 1 illustrates the PID graph as generated by [project FREYA](https://www.project-freya.eu/en/front-page) in August 2020 ([Cousijn et al. 2020](https://www.sciencedirect.com/science/article/pii/S2666389920302440)).
- + Diagram of the PID graph from project FREYA in August 2020 showing connections between research objects

@@ -19,7 +19,7 @@ The "certain class" criterion relates to the fact that not all data products are Besides these high-level data products there is a very long tail of custom data products; they are mostly those that were made to support a particular publication. Some data centers support the creation of data bundles based on the selection of parts of larger datasets, often supporting the creation of a DOI for this custom bundle. Creating records for these as they get cited would result in opening the floodgates for indexed data products in SciX. Clearly, that would not be a desirable outcome. This is the part where we need to nuance the indexing criterion. This nuance will come in the form of a "reuse criterion": only when a data product is cited a second time will a record be created. Figure 2 gives an indication of what to expect: it shows the citation count as a function of publication year for dataset records in NASA SciX. These are not the actual counts, currently in the system, but the estimated ones if we were to create a record for every cited DOI corresponding to a dataset. The actual counts are likely to be even higher.
- + Bar chart showing estimated citation count by publication year for dataset records in SciX if all cited DOIs were indexed
Figure 2. Estimated citation count as a function of publication year for dataset records in SciX @@ -79,7 +79,7 @@ Table 1: general queries for discovering indexed data products To illustrate finding answers to questions about individual data products, we look at the following record already indexed in SciX: ["The IVS data input to ITRF2014", published by GFZ Data Services, Helmoltz Centre, Potsdam, Germany](https://scixplorer.org/abs/2015ivs..data....1N/abstract). As of April 11 it has 46 citations. On the one hand, this dataset is relevant to VLBI observation, while on the other, it is relevant to geodesy, specifically to the International Terrestrial Reference System (ITRF). Is this reflected in the context of those 46 citations? The results in figure 3 (created using the SciX paper network) highlight that some of them relate to astrometry, while others focus on the pure geodesy part. The *Publications* facet shows a wide range in publication venues. Adding the filter *property:openaccess* shows that about 50% of the citing works are Open Access. Since this data product comes with rich metadata, a useful venue for further discovery could be the use of the *similar()* operator; based on textual similarity, what other records in NASA SciX could potentially be interesting if this data product is relevant to your research? Executing the query [similar(bibcode:2015ivs..data....1N)](https://scixplorer.org/search?q=similar(bibcode%3A2015ivs..data....1N)&sort=score+desc%2Cdate+desc&p=1) returns an extensive list of publications, many about VLBI, but also with wider geodesy applications. A narrower version of this query also returns interesting results: what data products or software records are similar to this data product? The query [similar(bibcode:2015ivs..data....1N) doctype:(dataset OR software)](https://scixplorer.org/search?q=similar(bibcode%3A2015ivs..data....1N)+doctype%3A(dataset+OR+software)&sort=score+desc%2Cdate+desc&p=1) will return these results. Naturally, many VizieR data catalogs are returned, but also a software records like ["SOFA: Standards of Fundamental Astronomy"](https://scixplorer.org/abs/2014ascl.soft03026I/abstract) and ["liulei/volks: VOLKS: VLBI Observation for the Localization of frb Keen Searcher"](https://scixplorer.org/abs/2019zndo...2565124L/abstract).
- + SciX paper network showing clusters of publications citing the IVS data input to ITRF2014 dataset
Figure 3. Paper network for the publications citing the data product "The IVS data input to ITRF2014" @@ -91,7 +91,7 @@ The collection of indexed data products that is the most suitable to use as an e Focusing on the [5,000 most recent VizieR data catalogs](https://scixplorer.org/search?q=topn(5000%2C+bibstem%3AyCat%2C+date+desc)&sort=score+desc%2Cdate+desc&p=1), we discover that they have been [cited by just under 800 publications](https://scixplorer.org/search?q=citations(topn(5000%2C+bibstem%3AyCat%2C+date+desc))&sort=citation_count+desc%2Cdate+desc&p=1); [close to 600 of these](https://scixplorer.org/search?q=citations(topn(5000%2C+bibstem%3AyCat%2C+date+desc))+property%3A(openaccess+data)&sort=citation_count+desc%2Cdate+desc&p=1) are Open Access publications with links to data. Figure 4 illustrates the range of topics covered by these publications by creating the Paper Network. The Publications facet for these citations shows that they mostly come from the well-known astronomy publication venues and the Institutions facet (see figure 4, right) indicates that the authors of the citing publications work at a wide range of locations. The citing publications are also represented in many bibliographic groups ("bibgroups"); these are curated lists of publications for institutes, missions or instruments.
- + Left: paper network for publications citing top 5000 VizieR catalogs. Right: Institutions and Bibgroups facets for citing publications
Figure 4. Left: Paper network for the publications citing the top 5000 most recent VizieR data catalogs. Right: Institutions and Bibgroups facets for the publications citing the top 5000 most recent VizieR data catalogs. diff --git a/_includes/_blogcontent/2025-02-27-scix-ambassador-workshop.md b/_includes/_blogcontent/2025-02-27-scix-ambassador-workshop.md index 36d4ffe9..3550a725 100644 --- a/_includes/_blogcontent/2025-02-27-scix-ambassador-workshop.md +++ b/_includes/_blogcontent/2025-02-27-scix-ambassador-workshop.md @@ -8,7 +8,7 @@ A key component of the workshop was the **blue sky project activity**, where amb - **Workshop Report Team** – Led by Stephanie Jarmak, Harper Wilkins, and Sunny Narayanan, this team is compiling key workshop discussions, feedback, and outcomes.
- + Group photo of SciX Lead Ambassadors and SciX staff at the end of the 2024 workshop in Cambridge, MA

diff --git a/_includes/_blogcontent/2025-02-27-scix-earth-science-literature-review.md b/_includes/_blogcontent/2025-02-27-scix-earth-science-literature-review.md index 9deadac2..2d346b91 100644 --- a/_includes/_blogcontent/2025-02-27-scix-earth-science-literature-review.md +++ b/_includes/_blogcontent/2025-02-27-scix-earth-science-literature-review.md @@ -7,7 +7,7 @@ When I search for literature on a search engine, my instinct is to type in a key The `abs:""` function of SciX can search my keywords in titles and also in the abstract and keywords sections. For example, I can type in the search bar on SciX `abs:(“Antarctica” AND “snowfall” AND “sea ice”)`, and SciX will go through the titles, abstracts, and keywords of records in the corpus to find the most relevant literature for these topics.
- + Screenshot of SciX search results using the abs: field for Antarctica, snowfall, and sea ice keywords

@@ -15,7 +15,7 @@ The `abs:""` function of SciX can search my keywords in titles and also in the a What blew my mind was that SciX actually works with publishers to obtain the full text in their metadata. Although you still often need your own way of access to the full text (for example, through an institutional subscription to a journal), on SciX regardless of institutional access you can search your keyword in the full text of literature using `full:""`, in a way similar to `abs:""`.
- + Screenshot of SciX search results using the full: field to search within the full text of literature

@@ -26,16 +26,16 @@ It’s happened to me often that my advisor would give me one paper that they th When I type “Wagner and Eisenman, 2015” in the SciX search bar, I can find the paper my advisor gave me. Here are some functions I would use to expand my search on this paper: 1. **`useful()`** is a function that asks what papers are cited by publications most relevant to my topic. In my example, I would type `useful(Wagner and Eisenman, 2015)` in the search bar, and it will show me what papers are cited by studies like Wagner and Eisenman 2015. These would be the studies that came before Wagner and Eisenman 2015 that this topic built upon. If I type just some keywords rather than metadata associated with a specific paper, it would provide records covering the foundation for this topic that authors cite. - +Screenshot of SciX search results using the useful() function to find foundational papers cited by relevant literature 2. **`reviews()`** is a function that finds the papers that include citations most relevant to my topic. When I use this function, I am going to find papers that came after Wagner and Eisenman and synthesize or build on top of their research, thus citing this research. - +Screenshot of SciX search results using the reviews() function to find papers that cite and build on relevant literature 3. **`trending()`** shows me the reader community of this topic. I can see what papers on this topic do SciX users read the most. Using this function is like how in your lab group, you might see what else people are reading that you might not have discovered yet. - +Screenshot of SciX search results using the trending() function to show most-read papers in a topic area 4. Finally, **`similar()`** helps me find papers that have similar content to this one paper I have. SciX compares abstracts and provides a robust way of discovering similar research when I have no idea who else is doing similar research in the field. - +Screenshot of SciX search results using the similar() function to find papers with similar content based on abstract comparison Using these four functions, I quickly identified many more papers that are very relevant to my research questions and expanded my one reading assignment to a more comprehensive reading list. @@ -45,7 +45,7 @@ As a graduate student, I often want to search for my advisor’s work or the pub SciX provides more advanced search filters that can help with the common name issue. First, on the left of the screen, the first filter is authors. If you click the checkbox of certain names, you can limit to or exclude those people. To further narrow down by name, you can click on the small arrow next to the names and expand to people with the same last name and first name initial, so you can distinguish them with their middle names. If someone changed their name throughout their career, you could click on multiple names in the `author` filter and limit the search results to multiple names.
- + Screenshot of the SciX author filter showing how to narrow search results by author name and middle initial

@@ -55,7 +55,7 @@ Another handy filter is `institutions`. Once you click on this filter, you can s With both the `author` and `institutions` filters, I can quickly narrow my search down to the right author I am looking for.
- + Screenshot of the SciX institutions filter showing how to narrow search results by author affiliation

@@ -64,7 +64,7 @@ With both the `author` and `institutions` filters, I can quickly narrow my searc My favorite function of SciX has to be their visualization tools for the search results. When I first entered the field, I wanted to identify who was publishing under the topic that I became interested in. The author network visualization generated when I search a certain topic such as “Antarctic Ice Sheet” can show me a color-coded pie-chart of different groups of people who tend to publish together. When I click on the `view link overlay` option, I can see the authorship collaborations between different groups. This is helpful for me to find out who is publishing often in the group and who collaborates with particular authors. This function can be very helpful when you are applying for graduate school to identify the big contributors in the field. The author network is also a powerful tool when you are trying to find collaborators in a field that you are not familiar with.
- + Author network visualization in SciX for the query 'Antarctic Ice Sheet', showing color-coded research groups and collaboration links

@@ -75,7 +75,7 @@ One piece of advice that I got from a professor was to subscribe to important ac On SciX, I can sign up for weekly or daily alerts that include the results of certain queries. To do this, once I search for specific keywords or authors I click on the little bell button on the top right of all my search results. It will prompt me to receive email notifications when new literature is added to the search result. This is a topic-specific and cross-journal method of keeping up-to-date with the literature of your interest.
- + Screenshot of SciX showing the email alert notification bell to subscribe to search result updates

diff --git a/_includes/_blogcontent/2025-03-25-what-i-wish-i-knew-about-ads-scix-during-my-phd.md b/_includes/_blogcontent/2025-03-25-what-i-wish-i-knew-about-ads-scix-during-my-phd.md index 90c822b4..f28df060 100644 --- a/_includes/_blogcontent/2025-03-25-what-i-wish-i-knew-about-ads-scix-during-my-phd.md +++ b/_includes/_blogcontent/2025-03-25-what-i-wish-i-knew-about-ads-scix-during-my-phd.md @@ -10,7 +10,7 @@ In this blog, I'll share some of my favorite Scix features that I wish I had kno ### 1- Astronomy is still a main area of support and interdisciplinary content is a feature and not a bug.
- + Screenshot of the SciX interface showing the discipline drop-down menu with Astrophysics selected

@@ -19,7 +19,7 @@ The classic form is still available for those who prefer it. You can access it b The inclusion of additional scientific disciplines in SciX creates new opportunities for cross-disciplinary collaboration and discovery. Just as in ADS, you can limit your search results to astronomy by using the filter ``collection:astronomy`` in your search query or by selecting "astronomy" under the filter options on the left side of the interface.
- + Screenshot of SciX search results filtered to astronomy collection using the collection:astronomy query

@@ -31,14 +31,14 @@ Your ADS account and account settings are fully integrated and shared with SciX, Libraries can be designated as public, shared, or private to suit your needs. **A feature currently exclusive to SciX** is the ability to add annotations to saved papers—extremely useful for documenting why you saved a particular paper in a specific library. This is one extra small reason to do the change from ADS to SciX and a reminder that future development will focus on the SciX platform and new features will be made available on SciX.
- + Screenshot of a SciX library showing papers with annotation notes added to saved entries

Make sure you have an account to be able to save papers to your libraries.
- + Screenshot of the SciX account sign-in prompt encouraging users to log in to save papers

@@ -71,7 +71,7 @@ Libraries can serve as input for the [4 second-order operators](https://ads.harv which you can further modify and explore.
- + Screenshot of the SciX library Explore menu showing second-order operator options including similar, trending, useful, and reviews

diff --git a/_includes/_blogcontent/2025-07-01-scix-visualizations.md b/_includes/_blogcontent/2025-07-01-scix-visualizations.md index 94d11799..775f7e78 100644 --- a/_includes/_blogcontent/2025-07-01-scix-visualizations.md +++ b/_includes/_blogcontent/2025-07-01-scix-visualizations.md @@ -2,7 +2,7 @@ I’m Sarah Lamm, a PhD candidate in the Geology Department at the University of This is why SciX is powerful: it pulls scientific references from multiple disciplines and brings them together in one searchable platform. After you’ve submitted a query in SciX, you have the option to visualize the results. Go to explore in the top right hand corner right above your results. You have six options: overview, metrics, author network, paper network, concept cloud, and results graph. But what’s the power in that? I love figures, graphs, and tables, and I know I'm not alone. Many people prefer a clear visual over reading long paragraphs of text. As the saying goes, a picture is worth a thousand words. That's why the visualization tools in SciX are my favorite feature, especially when I'm starting a new research topic. The SciX visualizations help me quickly identify key authors, papers, related topics, and even methodologies. This gives me a faster and more focused entry point into the current understanding of a subject. It allows me to move beyond just reading the most relevant, but possibly generic, results. -### When the Query is a Person (Name or ORCID) +## When the Query is a Person (Name or ORCID) Situation: You just overheard someone mention a scientist’s name at a conference, and you are about to meet them. Though the problem is you’ve never heard of them before, and you have less than 10 minutes to learn everything you can. What is their area of expertise? Are they still active in the field or just starting out? Are they highly cited? Do you know someone who can introduce you? How will you find all of this out quickly? @@ -14,7 +14,7 @@ See when someone started publishing and whether they’ve published recently—e - If they’re actively publishing or possibly scaling back - Whether they’re someone you might connect with as a peer or mentor
- + Timeline of publications chart in SciX showing an author's publication history over time

@@ -33,7 +33,7 @@ As someone who will soon be on the post-doc market, I will be looking for a post - See their areas of expertise and what they’ve been involved in over time - Spot trends in their research interests -### When the Query is a Topic or Set of Keywords +## When the Query is a Topic or Set of Keywords Problem: You’ve been assigned to collaborate on a project in an area where you have minimal expertise. Don’t panic, just head over to SciX. SciX shows you the key papers on a topic and the authors who have worked on it. - Paper Network @@ -45,7 +45,7 @@ Problem: You’ve been assigned to collaborate on a project in an area where you - The bigger the name, the more they’ve contributed.
- + Author network visualization in SciX for the query 'Aerogels', showing research groups and collaboration patterns

@@ -57,7 +57,7 @@ Individual authors can be selected to see how their specific work contributes to - Get a quick overview of what’s been explored. - See what’s been attempted or theorized. -### Pro Tip: Filter by Years +## Pro Tip: Filter by Years People and ideas change over time, so maybe you aren’t interested in every paper available. Visualizations even respond when filtered by year. How many scientists have changed research focus from when they were a student to their current career stage? If you don’t filter by year you are getting everything this ever worked on, which might not be useful. @@ -74,13 +74,13 @@ Same with topics, how many hypotheses have been thrown out over time, or have re - It’s a fast, effective way to get up to speed on current conversations in the field.
- + Two paper network visualizations for 'Titan Saturn Organics': left shows papers from 1973–1997, right shows papers from Cassini's arrival to present, illustrating the evolution of scientific thought

Paper Networks based on the query “Titan Saturn Organics” are a great example of the power of filtering by years. The paper network on the left shows papers from 1973, which is the first time these keywords show up, through to the launch of Cassini and Huygens in 1997. This represents some of scientists’ earliest hypotheses about organics on Titan, and these references were used to justify sending Cassini and Huygens. The paper network on the right includes everything after Cassini arrived at Saturn and goes up to today. The ideas about Titan organics clearly became more refined and specific during this time, with more detail, more variety, and a stronger grounding in actual data. This is exactly what filtering by years reveals: not just the progression of published work, but the evolution of scientific thought over time. -### Pro Tip: Trying to Find Advisors/Collaborators +## Pro Tip: Trying to Find Advisors/Collaborators I wish I knew about SciX when I was first applying to graduate school to find advisors names, instead of just googling planetary schools or asking for recommendations. But now SciX does exist! Many of us, when searching for graduate school advisors, are told, “Find a journal article that interests you, then see who wrote it, and contact them.” While this method can be effective, it is neither highly efficient nor consistently reliable. Searching “Mars Laser Calibration” on other databases lists the most relevant or most recent journal article. A single journal article might have 30 authors, yet it would be difficult to know which author(s) are experts on this topic and which author(s) primarily expertise is in another field though still contributed something to this article due to overlapping knowledge. Using other databases to find advisors is time consuming and more likely to miss some really great advisors. @@ -96,13 +96,13 @@ These steps should narrow it down to authors who have recently published, whethe - Though avoid a narrow time frame that is too recent, since students may be high on the author list. Someone with 5 to 10 years of experience on the topic is likely out of school and actively working in the field. 3. Finally, head over to the author network to see which names appear.
- + Author network in SciX for the query 'Mars Laser Calibration' from 2020–2025, highlighting the most published researchers in this area

Here is an author networked based on the query “Mars Laser Calibration” from 2020-2025. This shows who is the most published on this work in the past five years. This would be a great list to start on for advisors (or collaborators) if you want to work on Laser Calibrations useful for Mars research. From here you would need to find affiliations, because they might not be at a university and unable to take students. Some affiliations are listed in SciX, but not all. -### Conclusion +## Conclusion I love SciX because it offers a more effective way of identifying connected topics and relevant authors. Even if my own search methods didn’t miss anything during literature reviews, while developing methodologies, or when looking for a graduate advisor, they were undeniably time-consuming and outdated. At the very least, SciX would have saved me time, even if it led to the same results. But in reality, it likely would have done a better and more in-depth job. I’m an ambassador for SciX because I value efficiency and appreciate simple, powerful tools. More importantly, I’ve seen how academic research is filled with unwritten rules and hidden tools known only to a select few. It's deeply unfair that some of the “best” or “most productive” researchers are simply those who know how to access and use these tools. Research tools shouldn’t be kept secret, they should be shared openly. That’s why I’m a SciX ambassador: to help level the playing field for all researchers, not just the privileged. When everyone has access to the tools they need, we can focus on real science instead of wasting time trying to catch up. diff --git a/_includes/_blogcontent/2025-08-25-scix-data-collections.md b/_includes/_blogcontent/2025-08-25-scix-data-collections.md index ee678489..1ec774c8 100644 --- a/_includes/_blogcontent/2025-08-25-scix-data-collections.md +++ b/_includes/_blogcontent/2025-08-25-scix-data-collections.md @@ -5,20 +5,20 @@ As can be seen from the list of datasets displayed in the filter, data collectio In addition to being able to select records in a data collections by using the proper filter, one can also use the corresponding search constraint via the data field, e.g. `data:ORNL.DAAC` will return all records that belong to the NASA’s ORNL.DAAC collection.
- + Figure 1: SciX data filter showing available Earth science data collections on the left, and publication types for ORNL DAAC records on the right Figure 1: Left: Data collections currently available in SciX’s Earth science collection (`collection:earthscience`). Right: Publication types for records currently found in the ORNL DAAC data collection (`data:ORNL.DAAC`).

-### Contents +## Contents The records found in a given data collection consist of resources which either *are* datasets hosted by a particular repository or *use* data from a particular repository. The first category typically consists of high-level data products that are indexed in SciX. Examples of such records include ones found in the different NASA DAACs (original observations by NASA’s earth observing satellites) or the VizieR data products (machine readable datasets associated with astronomy articles), which have been indexed in the system to make them discoverable and citable. The second category includes data bibliographies which link articles to datasets hosted by the repositories. Examples include the SIMBAD and NED collections, which link articles to measurements of astronomical objects, and the collections from the astrophysics archives (MAST, Chandra, IRSA, HEASARC), which link papers to data products hosted by them. In order to distinguish between records which correspond to a dataset from the records of papers that use the dataset, one can simply use the “Publication Type” filter to see the different documents available in the particular collection. As an example, figure 1 shows the documents found in the ORNL DAAC data collection. -### Curation +## Curation All data collections in SciX are curated according to various criteria and various levels of effort. Historically, the collections associated with the data hosted by the astrophysics archives have been maintained by curators working at the different archives, and have relied on a meticulous analysis of the papers published in the scientific journals of interest to astronomers. (For more information on the process followed, please refer to [this publication](https://scixplorer.org/abs/2024OJAp....7E..85O/abstract)). @@ -26,21 +26,21 @@ With the advent of electronic publishing and the adoption of FAIR principles, mo In general, any given data collection may be composed by aggregating records which are curated by data managers collaborating with SciX, and records which are mined from the literature by the indexing pipelines implemented by SciX. As our full-text holdings in SciX increase and our ability to incorporate robust AI/ML methods in our pipelines improves, we expect to reduce the amount of human efforts needed to curate these collections long-term. -### Citations and Credits +## Citations and Credits One distinctive feature of SciX is to track citations between research works. While this has traditionally meant providing links between papers based on the list of formal citations found in their bibliography, it has now made it possible to also track citations between a paper and a data product or software records. This information is exposed in SciX via the “Citations” tab available in the left menu for each record, as shown in figure 2. However, thanks to our text mining efforts, we are now able to supplement this information with additional links between papers and datasets or software mined from the papers’ full-text (typically the so-called “data availability statement” sections). This provides an additional set of linkages between papers and data products mentioned in them which are named credits in SciX. This will become an additional impact metric that we will track for an increasingly larger number of research products such as data and software going forward.
- + Figure 2: SciX record for an ORNL DAAC dataset showing 139 citations and 2 credits from mentions, with citation metrics inset Figure 2: The SciX record for a dataset hosted by the ORNL DAAC. As of 8/25/2025, SciX has identified 139 citations and 2 credits from mentions for the dataset. Insert: the corresponding citation metrics for the record in question.

-### Concluding Remarks +## Concluding Remarks Tracking the use of research data and software in the scientific literature is one of the primary goals of SciX. This not only helps reproducibility of scientific results, but it also allows greater discoverability of all the research artifacts involved: papers, software, and datasets. An additional benefit of enhancing the FAIRness of this content is the ability for researchers, data managers, and funders alike to evaluate the scientific impact of people, projects and institutions. diff --git a/_includes/_blogcontent/2025-09-29-scix-launch.md b/_includes/_blogcontent/2025-09-29-scix-launch.md index 40a9ebb5..d5a9065f 100644 --- a/_includes/_blogcontent/2025-09-29-scix-launch.md +++ b/_includes/_blogcontent/2025-09-29-scix-launch.md @@ -27,7 +27,7 @@ SciX is a project created by the ADS team and operated out of the Smithsonian As ## Welcome aboard!
- + SciX launch announcement graphic

@@ -42,7 +42,7 @@ SciX is a project created by the ADS team and operated out of the Smithsonian As
-

Press Coverage

+

Press Coverage

    @@ -55,7 +55,7 @@ SciX is a project created by the ADS team and operated out of the Smithsonian As
    -

    Press Coverage

    +

    Press Coverage

    • New NASA-Backed Research Platform SciX Expands Open Science
      Center for Astrophysics | Harvard & Smithsonian
    • SciX: A New Era for NASA Research Discovery
      NASA Science Data Portal
      • @@ -133,7 +133,7 @@ SciX is a project created by the ADS team and operated out of the Smithsonian As margin-bottom: 15px; } - .press-coverage-header h4 { + .press-coverage-header h3 { margin: 0; font-size: 16px; font-weight: 600; diff --git a/_includes/_help/actions/_posts/export.md b/_includes/_help/actions/_posts/export.md index 595507ab..4b5a27a0 100644 --- a/_includes/_help/actions/_posts/export.md +++ b/_includes/_help/actions/_posts/export.md @@ -13,7 +13,7 @@ When the tool is opened, you will have the opportunity to review the export resu ### Export Formats Use this button to export your search results in different formats. Currently available options are: -###### 1. Tagged Formats: +#### 1. Tagged Formats: * BibTeX * BibTeX ABS * ADS (generic tagged abstracts) @@ -23,13 +23,13 @@ Use this button to export your search results in different formats. Currently a * RefWorks * MEDLARS -###### 2. LaTeX Formats: +#### 2. LaTeX Formats: * AASTeX * Icarus * MNRAS * Solar Physics (SoPh) -###### 3. XML Formats: +#### 3. XML Formats: * DC (Dublin Core) XML * REF-XML * REFABS-XML diff --git a/_includes/_help/actions/_posts/visualize.md b/_includes/_help/actions/_posts/visualize.md index a5f09e81..77fbcd23 100644 --- a/_includes/_help/actions/_posts/visualize.md +++ b/_includes/_help/actions/_posts/visualize.md @@ -49,7 +49,7 @@ Clicking on a group will also show you in the right pane the most commonly refer ### Results Graph When you look at a list of {{ include.site }} search results, you can sort by date published, by citation count, or by recent popularity of the article in {{ include.site }}, but you cannot see all of these dimensions at once, and you cannot easily see outliers. The results graph is a customizable scatter chart that allows you to assign values to the x and y axes as well as to the radius of the circle representing a paper. -{% if include.ads %}{% endif %} +{% if include.ads %}Scatter plot of search results showing date on x-axis, citation count on y-axis, and circle size representing recent reads{% endif %} #### How to use it @@ -64,7 +64,7 @@ The default graph shows the [recent views]({% if include.ads %}../actions/analyz ### Concept Cloud The concept cloud shows you **frequently appearing** and **unique words** in your search results. -{% if include.ads %}{% endif %} +{% if include.ads %}Word cloud of frequently appearing and unique keywords in a set of search results{% endif %} #### How the concept cloud is made The concept cloud takes words from the titles and abstracts of your search results, counts their frequencies and compares them to the same word's frequency across the entire {{ include.site }} corpus. @@ -76,5 +76,5 @@ The concept cloud takes words from the titles and abstracts of your search resul ### Instructions on Downloading Graphics as High-Quality PNGS in Chrome 1. Install the SVG Crowbar 2 Bookmarklet 2. Open the graph in {{ include.site }} (currently the paper and author networks have the best support) -3. Click the SVG Crowbar icon, you will see something that looks a bit messy, like this: {% if include.ads %}{% endif %} +3. Click the SVG Crowbar icon, you will see something that looks a bit messy, like this: {% if include.ads %}Screenshot of the SVG Crowbar bookmarklet overlay showing download buttons for network visualization charts{% endif %} 4. Click on the two bottom buttons: #network-viz-main-chart to download the main chart, and #network-viz-time-series to download the accompanying time series graph. diff --git a/_includes/_help/data_faq/_posts/data-faq.md b/_includes/_help/data_faq/_posts/data-faq.md index bc2bcd02..d400663e 100644 --- a/_includes/_help/data_faq/_posts/data-faq.md +++ b/_includes/_help/data_faq/_posts/data-faq.md @@ -5,28 +5,28 @@ ## General -##### Q: How often do new articles get added to the database? +### Q: How often do new articles get added to the database? This depends on the source. We ingest from arXiv daily; from astronomy journals and other sources weekly, over the weekend; and from physics journals and other sources about once every 3 weeks, also over a weekend. -##### Q: How do I submit missing articles or corrections to an existing article? Missing references? +### Q: How do I submit missing articles or corrections to an existing article? Missing references? * [Missing articles/corrections to existing article]({% if include.ads %}{{ site.ads_base_url }}/feedback/correctabstract{% else %}{{ site.scix_base_url }}/feedback/missingrecord{% endif %}) * [Missing references]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/feedback/missingreferences) * [Link two associated articles]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/feedback/associatedarticles) Note that these forms do not work if you're using the basic HTML version of {{ include.site }}, and occasionally, some users encounter errors when submitting these forms; [email us](mailto:{% if include.site == 'SciX' %}help@scixplorer.org{% else %}adshelp@cfa.harvard.edu{% endif %}) if you run into issues. -##### Q: My paper is visible at the publisher but not in {{ include.site }} yet. +### Q: My paper is visible at the publisher but not in {{ include.site }} yet. Published articles are added to the database at regular intervals; see the publishing schedule above. In addition, for most journals, we do not add the article until it has a published volume and page number. While we appreciate the early access versions, we have found that matching them after the fact and tracking all citations correctly is difficult to do correctly. If sufficient time has passed since the publication date and the article is still unavailable, it may be in a journal we don't index by default. It's also possible that the article has been added, but is not appearing the expected collection (astronomy or physics); this is generally the case if the article appears in a general science journal (Nature, Science) where we need keyword information to assign it to a specific collection. Finally, in rare cases deliveries from publishers are missing some articles. If you believe your article should be in the database already, [email us](mailto:{% if include.site == 'SciX' %}help@scixplorer.org{% else %}adshelp@cfa.harvard.edu{% endif %}) for help. -##### Q: What are bibliographic groups (bib groups)? These appear in a left-side filter. +### Q: What are bibliographic groups (bib groups)? These appear in a left-side filter. Bibliographic groups are hand curated by librarians and/or curators at various institutions and generally contain a list of publications produced by researchers at a given institution or using specific telescope(s). If you're a librarian or curator interested in curating a publicly available collection, [email us](mailto:{% if include.site == 'SciX' %}help@scixplorer.org{% else %}adshelp@cfa.harvard.edu{% endif %}). -##### Q: My name is incorrect in an {{ include.site }} record. +### Q: My name is incorrect in an {{ include.site }} record. We receive author names and other metadata directly from the publisher. First check that your name is correct on the published article; if it isn't, first contact the publisher directly to fix it with them. However, if your name is correct with the publisher and wrong in the {{ include.site }} database, [fill out this form]({% if include.ads %}{{ site.ads_base_url }}/feedback/correctabstract{% else %}{{ site.scix_base_url }}/feedback/missingrecord{% endif %}) and we'll correct it. -##### Q: My name has changed since I first started publishing. How can I ensure people find all of my papers when searching for my name? +### Q: My name has changed since I first started publishing. How can I ensure people find all of my papers when searching for my name? We offer three options; one or more of these may suit your needs. [Email us](mailto:{% if include.site == 'SciX' %}help@scixplorer.org{% else %}adshelp@cfa.harvard.edu{% endif %}) for help deciding which option(s) are best for you and for making any necessary updates: * We maintain a list of author synonyms, so searches for one author name return results for both names. Let us know all of the names you've published under to have your names added to this list. (Note that common name variations, such as publishing under your entire first name vs. just an initial, are already included in searches.) * You may also consider [registering for an ORCID ID]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}{% if include.ads %}/blog{% else %}/scixblog{% endif %}/orcid-claims) and using that to maintain a personal bibliography. @@ -34,61 +34,61 @@ We offer three options; one or more of these may suit your needs. [Email us](mai For more information, see our [name change policy]({% if include.ads %}../policies/name-changes{% else %}../policies-scix/name-changes{% endif %}). -##### Q: What journals and other material do you index? +### Q: What journals and other material do you index? Complete lists of the journals, conferences, and other sources we index may be found [here]({% if include.ads %}http://adsabs.harvard.edu/abs_doc/journal_abbr.html{% else %}{{ site.scix_base_url }}/journalsdb{% endif %}). -##### Q: What papers do you have the full text for? +### Q: What papers do you have the full text for? In general, we have searchable full text for most major journals in astronomy and physics, especially recent volumes. This includes articles in the arXiv. -##### Q: How do I get my conference proceeding in {{ include.site }}? +### Q: How do I get my conference proceeding in {{ include.site }}? Full instructions for submitting conference proceedings can be found [here]({% if include.ads %}../data_faq/conf_proc{% else %}../data_faq-scix/conf_proc{% endif %}). -##### Q: Why is my citation count different on other platforms? +### Q: Why is my citation count different on other platforms? While we do our best to capture citations accurately, there are a few reasons we would have more or fewer citations than you may see on other platforms. The primary reasons are as follows: - We merge the arXiv record with the published record, so that a citation for either version counts as one citation. This avoids double counting a citation. - Citations to books, book chapters, and other less formally structured content is often difficult to resolve in an automated fashion. Our citations to this content is likely under-counted. - In order for a citation to count in our system, both the cited record and the citing record must be in our system. Users are always welcome to submit missing content through the [Missing articles]({% if include.ads %}{{ site.ads_base_url }}/feedback/correctabstract{% else %}{{ site.scix_base_url }}/feedback/missingrecord{% endif %}) form linked off our feedback menu. ## arXiv -##### Q: My arXiv paper is missing its references. +### Q: My arXiv paper is missing its references. We extract references directly from the PDF for arXiv records, which doesn't always work well, depending on reference and document format. If the paper will be published, we will get the reference list from the publisher and will update the references on the record at that point. Note also that we're working on a new module for extracting references directly from PDFs and arXiv reference extraction should improve at that point. -##### Q: My arXiv paper had some citations before it was published. Will these be lost once the published version is out? +### Q: My arXiv paper had some citations before it was published. Will these be lost once the published version is out? We automatically merge the arXiv and published versions of papers, including citations. -##### Q: The author list of the arXiv and the published versions of my paper are different. What happens when the two versions are merged? +### Q: The author list of the arXiv and the published versions of my paper are different. What happens when the two versions are merged? Author metadata from the published version takes precedence, so arXiv-only coauthors will be removed from the record. -##### Q: The published version of my paper is out and indexed on {{ include.site }}, but the arXiv version is listed separately. +### Q: The published version of my paper is out and indexed on {{ include.site }}, but the arXiv version is listed separately. The published and the arXiv versions of a paper should merge into a single entry automatically. Occasionally that doesn't work; [let us know]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/feedback/associatedarticles) and we'll fix it. -##### Q: My name is correct on arXiv but wrong in {{ include.site }}. How can I fix it? +### Q: My name is correct on arXiv but wrong in {{ include.site }}. How can I fix it? Submit your corrections using [this form]({% if include.ads %}{{ site.ads_base_url }}/feedback/correctabstract{% else %}{{ site.scix_base_url }}/feedback/missingrecord{% endif %}). -##### Q: My name is wrong in arXiv, will you fix it? +### Q: My name is wrong in arXiv, will you fix it? You'll need to contact the arXiv directly for corrections to your papers on their site. ## Refereed status -##### Q: Why is my PhD thesis listed as refereed? +### Q: Why is my PhD thesis listed as refereed? {{ include.site }} has decided to list PhD theses as refereed because they go under the review of a thesis committee and are thus "peer reviewed." However, if you prefer to not see PhD theses appear in your search results, restrict your search results to articles only using the "Publication Type" filter in the left-side column. -##### Q: A conference proceeding is listed as non-refereed even though it underwent peer review. +### Q: A conference proceeding is listed as non-refereed even though it underwent peer review. Most conference proceedings are not refereed. They may be reviewed by an editor, but rarely is there the kind of rigorous review as is done by many journals. (In general, users and editors and librarians and publishers all have different opinions on what constitutes "peer-reviewed.") If a publication or a conference is generally not peer-reviewed, all articles/proceedings within that publication/conference will automatically be listed as non-refereed. If a particular article/proceeding within the generally non-refereed publication/conference is peer-reviewed, have the editors [email us](mailto:{% if include.site == 'SciX' %}help@scixplorer.org{% else %}adshelp@cfa.harvard.edu{% endif %}) to confirm and we can correct the listing. ## Submissions -##### Q: How do I submit my PhD thesis? +### Q: How do I submit my PhD thesis? Some institutions send us their recent PhD theses directly, though it may take a few months post-defense for us to receive them. However, if your institution does not send us your thesis, you have several options to add it to our database: * [Zenodo Astronomy Thesis](https://zenodo.org/communities/astrothesis) collection: This is an open-source repository of astronomy theses and dissertations which is automatically ingested into {{ include.site }} roughly once a month. If your thesis is already indexed by {{ include.site }} but the text is not openly accessible, you can upload a copy of the PDF to make it openly available. This is a good option if you'd like your thesis to be openly available and it's not currently accessible online. * [{{ include.site }} submission]({% if include.ads %}{{ site.ads_base_url }}/feedback/correctabstract{% else %}{{ site.scix_base_url }}/feedback/missingrecord{% endif %}): You can submit your thesis metadata directly to {{ include.site }} for indexing. If you want the PDF to be linked to the record, it will first need to be hosted somewhere online and then you can provide the URL and other metadata using this form. If the text of your thesis is not already available online and you'd like it to be, consider submitting it to the Zenodo collection. -##### Q: My name (or title, etc.) is misspelled on my paper. +### Q: My name (or title, etc.) is misspelled on my paper. If it is wrong on the publisher's website, you'll need to contact them to correct the error, as we've agreed with the publishers to reflect the data they pass on to us. If it's right on the publisher's website but wrong on ours, we're sorry for the error! [Contact us]({% if include.ads %}{{ site.ads_base_url }}/feedback/correctabstract{% else %}{{ site.scix_base_url }}/feedback/missingrecord{% endif %}) so we can fix it. -##### Q: How can I get my software package indexed in {{ include.site }}? +### Q: How can I get my software package indexed in {{ include.site }}? Software records are automatically indexed in {{ include.site }} once they have a Zenodo record and have been cited at least once. If you'd like to make your software records eligible for indexing in {{ include.site }}, complete the following steps: 1. Upload your software code to [Zenodo](https://zenodo.org/). You can do this directly or by linking to a Github repository. If you link to a Github repository, you can specify a specific release or version, or you can link to the top-level repository to create a non-version-specific record. 2. Get the BibTeX (or other bibliographic format) record from Zenodo and cite it in your paper as normal. Your software will not yet be in {{ include.site }}, so make sure to get the citation information from Zenodo. @@ -98,5 +98,5 @@ Some things to keep in mind: * Zenodo allows you to create different records for different versions of your software, which generally correspond to different releases in Github. This can be beneficial if the software has changed substantially with time, or if different authors have worked on different versions of the code and need to be acknowledged as appropriate. {{ include.site }} will index each Zenodo version of your software separately, as long as each has citations. Currently, citations are counted for each version separately, but eventually it will be possible to see all citations for all versions of a software package in one record in {{ include.site }}. * The [Astrophysics Source Code Library](http://ascl.net) indexes astronomy-related software that has been used in a publication. {{ include.site }} indexes these ASCL records (bibstem: [ascl]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}{% if include.ads %}/#search/q={% else %}/search?q={% endif %}bibstem%3A%22ascl%22&sort=date%20desc%2C%20bibcode%20desc&p_=0), publication type: [software]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}{% if include.ads %}/#search/q={% else %}/search?q={% endif %}doctype%3Asoftware&sort=date%20desc%2C%20bibcode%20desc&p_=0)) and they can collect citations similarly to the process above. One difference between the two processes is that ASCL indexes only the non-version-specific record while Zenodo indexes each version separately. It is possible for a given software package to be in both Zenodo and ASCL, if they fit the necessary criteria for each. -##### Q: I submitted some ORCID claims but they don't show up when I search by my ORCID ID. +### Q: I submitted some ORCID claims but they don't show up when I search by my ORCID ID. These can take up to 24 hours to index. Please [contact us](mailto:{% if include.site == 'SciX' %}help@scixplorer.org{% else %}adshelp@cfa.harvard.edu{% endif %}) if they aren't showing up after this time. diff --git a/_includes/_help/faq/_posts/faqs.md b/_includes/_help/faq/_posts/faqs.md index 6b9c3798..a9cd867a 100644 --- a/_includes/_help/faq/_posts/faqs.md +++ b/_includes/_help/faq/_posts/faqs.md @@ -4,28 +4,28 @@ ## Searching -##### Q: Typing a fielded query for an author query (e.g. author:"huchra, j." or author:"^huchra, j.") or clicking on the search term dropdown is a lot of work. +### Q: Typing a fielded query for an author query (e.g. author:"huchra, j." or author:"^huchra, j.") or clicking on the search term dropdown is a lot of work. There are two options. First, a first-author query can usually be entered as *^huchra, j.*---the *author:* tag is not necessary for first-author searches (note, though, that this format does not work well for authors with multi-part last names). Second, many search tags will autocomplete in the search box. Begin typing the search tag, such as *author:*, and either press the return key or the right arrow key when the tag autocompletes to accept it. -##### Q: Is it possible to search using the second author of a paper? +### Q: Is it possible to search using the second author of a paper? Positional searches are supported. To search for a second author, use *pos(author:"huchra,j.",2)*. See the Help page for [positional field searches]({% if include.ads %}../search/positional{% else %}../search-scix/positional{% endif %}) for more info. -##### Q: How do I exclude a term from my search? +### Q: How do I exclude a term from my search? Either prepend a negative sign (e.g. *-doctype:"proposal"*) or use the Boolean operator NOT (e.g. *NOT doctype:"proposal"*) while searching. See the Help page for [Boolean queries]({% if include.ads %}../search/search-syntax#combining-search-terms-to-make-a-compound-query{% else %}../search-scix/search-syntax#combining-search-terms-to-make-a-compound-query{% endif %}) for more info, paying special attention to the note on when differences in behavior between NOT and the negative sign may arise. -##### Q: Records are missed when searching from the 1st of one month to the end of the current month, e.g. pubdate:[2016-01-01 TO 2016-06-30]. +### Q: Records are missed when searching from the 1st of one month to the end of the current month, e.g. pubdate:[2016-01-01 TO 2016-06-30]. Records do not generally have a publication day, just a month and year. The missing day is set to 00 (e.g. January 2016 is set to 2016-01-00). Searches starting on the 1st of a given month will exclude all records with publication days of 00. It is preferable to not use a day when searching over a publication date range; specifying only a month will include records with publication days of 00. This is similarly true for the small number of records missing publication months. Searches beginning in January of a given year may miss records with publication months of 00. To search for records from the first half of the year, employ a search term such as *pubdate:[2016 TO 2016-06]*. -##### Q: How can I search for an acronym that is the same as a common word? +### Q: How can I search for an acronym that is the same as a common word? {{ include.site }} treats search terms entered in all caps as acronyms and will only return records that contain the all caps acronym form, not the lowercase common word form. In addition, some acronyms will auto-expand in the search (e.g. searching for "ADS" will find both "ADS" and "Astrophysics Data System" but will ignore "ads"). -##### Q: My new paper is not appearing in {{ include.site }}. +### Q: My new paper is not appearing in {{ include.site }}. New papers appearing on arXiv are ingested daily, though there may be a delay of one day for them to appear in the new {{ include.site }}. Published articles are ingested as the publisher provides them on a weekly basis, generally over the weekend. -##### Q: Searching for an author's name plus their affiliation doesn't give a complete list of results. +### Q: Searching for an author's name plus their affiliation doesn't give a complete list of results. Not all publishers provide authors' affiliations for search indexing, even if the affiliations are listed in the PDF or HTML form of the article itself. Also, note that searching using the *aff:* search tag searches the raw affiliation text provided by the publisher, such that searching for "Harvard-Smithsonian Center for Astrophysics" or for "CfA" will give different results. Use the *inst:* search tag to search the canonical affiliations; more information is available on the [Search Syntax help page]({% if include.ads %}../search/search-syntax{% else %}../search-scix/search-syntax{% endif %}). -##### Q: How do I build a URL using a known identifier of a paper? +### Q: How do I build a URL using a known identifier of a paper? You can access the abstract page of a known paper by inserting an identifier (bibcode, DOI, arXiv ID) into a URL, following a set pattern. The base URL is `{% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/abs/`, where `` can be one of the following: * bibcode, e.g. [{% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/abs/2008ApJ...689.1044G]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/abs/2008ApJ...689.1044G) * DOI, e.g. [{% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/abs/10.1086/592738]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/abs/10.1086/592738) @@ -34,22 +34,22 @@ You can access the abstract page of a known paper by inserting an identifier (bi * [{% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/abs/0808.2870]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/abs/0808.2870) {% if include.ads %}## Submitting Grant Applications -##### Q: My NSF grant application requires that I provide a list of all of my recent co-authors. Can {{ include.site }} provide that list? +### Q: My NSF grant application requires that I provide a list of all of my recent co-authors. Can {{ include.site }} provide that list? We have a tool specifically for this purpose: the "Author Affiliation" report option on the Export menu (accessible from the search results page). For more, see the [Author Affiliation help page]({% if include.ads %}{{ site.ads_base_url }}/help/actions{% else %}{{ site.scix_base_url }}/scixhelp/actions-scix{% endif %}/author-affiliation). -##### Q: My NSF application requires I build a CV via SciENcv. Can {{ include.site }} help with that? +### Q: My NSF application requires I build a CV via SciENcv. Can {{ include.site }} help with that? There are two options to use {{ include.site }} to help build your SciENcv: 1. The first option is to export your publications from {{ include.site }} in the [RIS format]({% if include.ads %}{{ site.ads_base_url }}/help/actions{% else %}{{ site.scix_base_url }}/scixhelp/actions-scix{% endif %}/export). The SciENcv citations manager will then allow you to import your citations in this format. 2. The second option is to link your ORCID account with SciENcv and import your citations from there. You can use {{ include.site }} to [add citations to your ORCID profile]({% if include.ads %}{{ site.ads_base_url }}/help/orcid{% else %}{{ site.scix_base_url }}/scixhelp/orcid-scix{% endif %}/claiming-papers), then link your updated ORCID profile to your account in SciENcv.{% endif %} {% if include.ads %}## Transitioning from Classic -##### Q: How do I transfer a private library from Classic to the new {{ include.site }}? +### Q: How do I transfer a private library from Classic to the new {{ include.site }}? Link your Classic account to your the new {{ include.site }} account and [use our import tool to transfer your library](../libraries/legacy-importing#importing-libraries). {% endif %} -##### Q: I have some links to Classic pages on my website - do I need to update all of these to the new {{ include.site }} links? +### Q: I have some links to Classic pages on my website - do I need to update all of these to the new {{ include.site }} links? Nope! Existing Classic URLs now redirect to the corresponding URLs in the new {{ include.site }}. -##### Q: Where do I find the utility ***Get citation lists for selected articles*** and similar second order queries? +### Q: Where do I find the utility ***Get citation lists for selected articles*** and similar second order queries? In general, the function **Reviews** in the **Explore** menu will generate the same list of publications as selecting all records in Classic and clicking on the button *Get citation lists for selected articles*. The only difference is the fact that the new {{ include.site }} does not show the frequency, but the results are sorted by the number of cites to the original set (when sorted by score). The new function **Useful** can be used in a similar way to generate the same results you would get the with button *Get reference lists for selected articles* in the old {{ include.site }}. When "score" is selected for sorting, the records are sorted by the number of cites by the original set. @@ -57,38 +57,38 @@ The new function **Useful** can be used in a similar way to generate the same re The **Co-reads** function corresponds with *Get also-read lists for selected articles*. ## {{ include.site }} Libraries -##### Q: The number of papers listed in the header of my library differs from the actual number in the library. +### Q: The number of papers listed in the header of my library differs from the actual number in the library. When you create or update your library, the bibcodes of the new records are stored in a database. Currently this list does not get updated when records are merged or deleted within the {{ include.site }} index, rather these changes get reflected at display time of the contents of an {{ include.site }} Library. ## ORCID -##### Q: I just claimed some papers using my ORCID ID but they're not showing up in the public search. +### Q: I just claimed some papers using my ORCID ID but they're not showing up in the public search. ORCID claims can take up to 24 hours to be processed and approved in our system. Please check the search again tomorrow. -##### Q: I have records on my ORCID profile that do not appear in {{ include.site }}. +### Q: I have records on my ORCID profile that do not appear in {{ include.site }}. First, if you haven't yet, you'll need to log into ORCID in {{ include.site }}, using the ORCID dropdown menu in the top bar. If you've published under multiple names, you'll need to enter these on your [ORCID settings page]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/user/settings/orcid). Papers on your ORCID profile also need to exist in {{ include.site }} and need to have an identifier we recognize (generally a bibcode, arXiv ID, or DOI). Finally, if you've recently entered or updated these records, note that it can take up to 24 hours for them to be registered in our system. ## Data and Curation For data and curation questions, see our [data and curation FAQs]({% if include.ads %}../data_faq/data-faq{% else %}../data_faq-scix/data-faq{% endif %}). ## Database Coverage -##### Q: How complete is {{ include.site }}? +### Q: How complete is {{ include.site }}? {% if include.ads %}{{ include.site }} aims to be the complete and authoritative source for the astrophysics literature. This includes not only published refereed articles and arXiv e-prints, but also the gray literature, comprised of conference proceedings, books, proposals, etc. We aim to not only index these resources but also enrich them with links to data or other resources when available. We also index published refereed papers and conferences that are likely to be cited by the core astrophysics literature, such as papers from physics, geophysics, and planetary science. If a record is missing, please let us know via our [Submit Abstract Form]({{ site.ads_base_url }}/feedback/correctabstract).{% else %}{{ include.site }} aims to be a comprehensive source for scientific literature. This includes published refereed articles and arXiv e-prints, as well as conference proceedings, books, and other scholarly works. We aim to not only index these resources but also enrich them with links to data or other resources when available. If a record is missing, please let us know via our [Submit Abstract Form]({{ site.scix_base_url }}/feedback/correctabstract).{% endif %} -##### Q: Why are citations from an arXiv record missing? Why is an arXiv record missing its references? +### Q: Why are citations from an arXiv record missing? Why is an arXiv record missing its references? For arXiv sources, we attempt to extract references from the full text and from there create citations. However, as papers can be submitted to the arXiv with a bibliography in a non-standard format, this process is not always successful. When the published version of an arXiv paper becomes available, we will use the publisher-provided reference list and disregard the arXiv reference list. -##### Q: For how many records is the full text available for searching? +### Q: For how many records is the full text available for searching? The full text is available for searching for many records, including most recent publications. You can search for records with full text using the query [has:body]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}{% if include.ads %}/#search/q=has:body{% else %}/search?q=has:body{% endif %}). Note that the searchable full text resides in our database and is separate from the links to publisher or arXiv sources; not all records with source links have searchable full text. ## Other -{% if include.ads %}##### Q: I'm trying to use the new interface but I'm getting a message about JavaScript / it's stuck on a loading screen. +{% if include.ads %}### Q: I'm trying to use the new interface but I'm getting a message about JavaScript / it's stuck on a loading screen. This issue is commonly seen when users have JavaScript turned off in their browser, or they're using security software or browser plugins (such as NoScript) that block JavaScript, or are accessing the site from a network that blocks content from certain domains (e.g. google.com). The full version of the new {{ include.site }} requires JavaScript in order to function (note: the basic HTML version, linked from the bottom of the search page or from the loading page when JavaScript is not detected, offers limited functionality without requiring JavaScript). At an absolute minimum you must have JavaScript turned on. Further, if you have any security settings or plugins that require sites to be whitelisted before running JavaScript, you must whitelist two domains for basic functionality: harvard.edu, and google.com.{% endif %} -##### Q: What internet browsers are supported by {{ include.site }}? +### Q: What internet browsers are supported by {{ include.site }}? We support all current versions (within the last 5 years) of Chrome, Firefox, Safari, and Edge. We also support Internet Explorer 11. This includes Firefox ESR (extended service release) versions, but does not include versions of any browser newer than 5 years old that have been officially retired. -##### Q: How should I acknowledge {{ include.site }}? +### Q: How should I acknowledge {{ include.site }}? If you wish to acknowledge us in a publication, kindly use a phrase such as the following: {% if include.ads %}"This research has made use of the Astrophysics Data System, funded by NASA under Cooperative Agreement 80NSSC21M00561."{% else %}"This research has made use of SciX, a scientific literature search and discovery platform."{% endif %} If you are using {{ include.site }} as a tool for bibliometric studies, please make sure you have an in-depth understanding of the system, its features and limitations, by reading and citing as appropriate the relevant published literature about {{ include.site }} ([refereed]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/public-libraries/aI9-ox_2RNeZK-gm-4DpVQ), [non-refereed]({% if include.ads %}{{ site.ads_base_url }}{% else %}{{ site.scix_base_url }}{% endif %}/public-libraries/iETdWs2pSGajhFBI30X3UQ)). -{% if include.ads %}##### Q: Do you have any mirror sites? +{% if include.ads %}### Q: Do you have any mirror sites? No, once we moved our site to the cloud in 2018, we no longer host mirror sites. See our [mirror policy page](../policies/mirrors) for more information.{% endif %} diff --git a/_includes/_help/gettingstarted/_posts/build-library.md b/_includes/_help/gettingstarted/_posts/build-library.md index 3146512b..88e52ee5 100644 --- a/_includes/_help/gettingstarted/_posts/build-library.md +++ b/_includes/_help/gettingstarted/_posts/build-library.md @@ -22,9 +22,9 @@ The same function is available on the abstract page of a single paper. The contents of a library can be [exported in a variety of formats]({% if include.ads %}../actions/export{% else %}../../actions-scix/export{% endif %}), including BibTeX and AASTeX. This was designed to facilitate the development of a {{ include.site }} library as a bibliography for a paper in progress, and allow its export into the appropriate format for the journal when ready. {% if include.ads %}
      - + Screenshot of a library showing the Export button and format selection dropdown
      {% else %}
      - + Animated image showing how to export a library in SciX using the Export button
      {% endif %} {% if include.ads %} @@ -32,7 +32,7 @@ The contents of a library can be [exported in a variety of formats]({% if includ The [library citation helper](../libraries/citation-helper) is a unique feature specifically available to help build and maintain complete collections. It's designed to evaluate the papers already in a library and suggest related papers that should possibly also be included.
      - + Screenshot of the library citation helper suggesting related papers not yet in the library
      {% endif %} @@ -40,16 +40,16 @@ The [library citation helper](../libraries/citation-helper) is a unique feature The [citations and read statistics]({% if include.ads %}../actions/analyze{% else %}../../actions-scix/analyze{% endif %}) for a library are available, similar to those available from the search results page or an abstract page. Click on the Metrics button within the library to view. {% if include.ads %}
      - + Screenshot of library metrics view showing citation and read statistics charts
      {% else %}
      - + Animated image showing how to access library metrics in SciX
      {% endif %} ### Visualizations: paper network, author network, word cloud The same [visualizations]({% if include.ads %}../actions/visualize{% else %}../../actions-scix/visualize{% endif %}) available in the search results page are available within a {{ include.site }} library. {% if include.ads %}
      - + Screenshot of the author network visualization showing color-coded groups of collaborating authors
      {% else %}
      - + Animated image showing the author network visualization in SciX
      {% endif %} diff --git a/_includes/_help/gettingstarted/_posts/searching-for-paper.md b/_includes/_help/gettingstarted/_posts/searching-for-paper.md index 06c34769..78b7bfad 100644 --- a/_includes/_help/gettingstarted/_posts/searching-for-paper.md +++ b/_includes/_help/gettingstarted/_posts/searching-for-paper.md @@ -52,7 +52,7 @@ Note: for a first-author search using the ^ operator, you do not have to specify If your search by author and/or publication year returns too many results, you can use [interactive filtering]({% if include.ads %}../search/filter{% else %}../../search-scix/filter{% endif %}) to narrow down the results instead of editing your original search query. Filtering by author or publication is often useful when a paper is known. {% if include.ads %}
      - + Screenshot of search results page with the author filter facet panel open in the left sidebar
      {% else %}
      - + Screenshot of SciX search results page with the author filter facet panel open in the left sidebar
      {% endif %} diff --git a/_includes/_help/index.md b/_includes/_help/index.md index 56ced8f5..7bed66ab 100644 --- a/_includes/_help/index.md +++ b/_includes/_help/index.md @@ -9,6 +9,6 @@
      - +
      diff --git a/_includes/_help/terms/_posts/terms-of-use.md b/_includes/_help/terms/_posts/terms-of-use.md index d5c16669..7c43b151 100644 --- a/_includes/_help/terms/_posts/terms-of-use.md +++ b/_includes/_help/terms/_posts/terms-of-use.md @@ -10,7 +10,7 @@ Use of {{ include.site }} services implies that the user has read and agrees to 4. {{ include.site }} makes reasonable efforts to ensure that the contents of its archives are accurate. However, {{ include.site }} does not guarantee the completeness, accuracy or usefulness of its databases and search interfaces. {{ include.site }} is not to be considered liable for any delay, downtime, or other failure of performance in providing its services. -### Acknowledgements +## Acknowledgements If you wish to acknowledge the services provided by {{ include.site }} in a publication, kindly use a phrase such as the following: diff --git a/_includes/_help/userpreferences/_posts/myads.md b/_includes/_help/userpreferences/_posts/myads.md index bbe34f1b..723cb6f3 100644 --- a/_includes/_help/userpreferences/_posts/myads.md +++ b/_includes/_help/userpreferences/_posts/myads.md @@ -8,7 +8,7 @@ The my{{ include.site }} notification service delivers daily or weekly email upd {% if include.ads == true %}
      - +
      {% endif %} @@ -20,7 +20,7 @@ To create a new notification (for all notifications except for the general notif {% if include.ads == true %}
      - + Screenshot of the myADS setup page showing options to create or import notification settings
      {% endif %} @@ -28,7 +28,7 @@ To create a new notification (for all notifications except for the general notif The arXiv notifications are designed as a replacement to the daily arXiv emails generated by Classic. They are generated daily on weekdays and notify you of all new papers in a selected set of arXiv categories or sub-categories. Optionally, you can also specify keywords to be notified of any new papers that match those keywords in your designated categories. During setup, you'll be asked to select your arXiv categories and specify any keywords, as desired.
      - + Screenshot of the arXiv notification setup screen with category and keyword selection fields

      @@ -42,7 +42,7 @@ Things to note during setup: The citations notifications provide a list of papers citing the articles written by a person, typically you; they are similar to the Classic {{ include.site }} “citations” list. They are generated weekly over the weekend and notify you of up to 5 papers that cite work by you or another specified author. Only new citations are shown.
      - + Screenshot of the citations notification setup screen with author name and ORCID ID fields

      @@ -57,7 +57,7 @@ The authors notifications are generated weekly over the weekend and notify you o The keywords notifications are generated weekly over the weekend and notify you of newly added papers about a given set of keywords or other query. Three queries are constructed for the given search term(s): recent papers, trending papers, and useful papers. Recent papers shows the 5 most recent papers matching the given query, while trending papers shows the 5 papers that best match the query *[trending]({% if include.ads %}../search/second-order{% else %}../search-scix/second-order{% endif %})(query)*. Useful papers shows the 5 papers that best match the query *[useful]({% if include.ads %}../search/second-order{% else %}../search-scix/second-order{% endif %})(query)*.
      - + Screenshot of the keywords notification setup screen with a search query input field

      @@ -69,7 +69,7 @@ Things to note during setup: The general notifications are new and did not have an equivalent in the Classic notification system. They allow users to create a notification out of almost any {{ include.site }} query. To set one up, execute a search that you'd like to receive notifications for, including any desired filters from the left sidebar. On the search results page,{% if include.ads %} click on the bar labeled **Create Email Notification** in the right sidebar.{% else %} click the bell/notification icon above the search results.{% endif %}
      - + Screenshot of the general notification setup widget showing a query name field and daily or weekly schedule options

      @@ -92,14 +92,14 @@ Detail-level settings, accessed via the Edit button as described above, are disp You import your Classic my{{ include.site }} settings using the provided import tool. From the [my{{ include.site }} setup screen]({% if include.ads %}https://ui.adsabs.harvard.edu/user/settings/myads{% else %}https://scixplorer.org/user/notifications{% endif %}), click the Import button.
      - + Screenshot of the myADS setup page showing the Import button for importing Classic myADS settings

      Enter your Classic username and password along with the mirror your account was registered on and click **Login** to complete your sign-in. (If you’ve forgotten your Classic password, recover it [here]({% if include.ads %}http://adsabs.harvard.edu/cgi-bin/nph-manage_account{% else %}https://scixplorer.org/help{% endif %}).)
      - + Screenshot of the Classic myADS login screen with username, password, and mirror selection fields

      diff --git a/_includes/_help/videos/_posts/advanced-search.md b/_includes/_help/videos/_posts/advanced-search.md index 354d3254..b32a25b9 100644 --- a/_includes/_help/videos/_posts/advanced-search.md +++ b/_includes/_help/videos/_posts/advanced-search.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for May 7, 2019, by Michael Kurtz, {{
      - +
      diff --git a/_includes/_help/videos/_posts/affiliations.md b/_includes/_help/videos/_posts/affiliations.md index 1da60b6e..958d3901 100644 --- a/_includes/_help/videos/_posts/affiliations.md +++ b/_includes/_help/videos/_posts/affiliations.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for April 23, 2019, by Carolyn Stern
      - +
      diff --git a/_includes/_help/videos/_posts/api.md b/_includes/_help/videos/_posts/api.md index 4d751483..fe8bb460 100644 --- a/_includes/_help/videos/_posts/api.md +++ b/_includes/_help/videos/_posts/api.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for June 4, 2019, by Kelly Lockhart
      - +
      diff --git a/_includes/_help/videos/_posts/experts.md b/_includes/_help/videos/_posts/experts.md index b93e426d..891d3f85 100644 --- a/_includes/_help/videos/_posts/experts.md +++ b/_includes/_help/videos/_posts/experts.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for June 25, 2019, by {{ include.site
      - +
      diff --git a/_includes/_help/videos/_posts/fulltext.md b/_includes/_help/videos/_posts/fulltext.md index 7bd80b76..fa3ee72e 100644 --- a/_includes/_help/videos/_posts/fulltext.md +++ b/_includes/_help/videos/_posts/fulltext.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for May 21, 2019, by Sergi Blanco-Cua
      - +
      diff --git a/_includes/_help/videos/_posts/infrastructure.md b/_includes/_help/videos/_posts/infrastructure.md index 1b7d0e54..1b5025ce 100644 --- a/_includes/_help/videos/_posts/infrastructure.md +++ b/_includes/_help/videos/_posts/infrastructure.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for April 9, 2019, by Sergi Blanco-Cu
      - +
      diff --git a/_includes/_help/videos/_posts/intro.md b/_includes/_help/videos/_posts/intro.md index 92c5f748..549c9a28 100644 --- a/_includes/_help/videos/_posts/intro.md +++ b/_includes/_help/videos/_posts/intro.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for March 12, 2019, by Kelly Lockhart
      - +
      diff --git a/_includes/_help/videos/_posts/libraries.md b/_includes/_help/videos/_posts/libraries.md index 0b2e160c..89837b44 100644 --- a/_includes/_help/videos/_posts/libraries.md +++ b/_includes/_help/videos/_posts/libraries.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for July 30, 2019, by Edwin Henneken
      - +
      diff --git a/_includes/_help/videos/_posts/personalization.md b/_includes/_help/videos/_posts/personalization.md index 8f8d21cf..6c07c2ce 100644 --- a/_includes/_help/videos/_posts/personalization.md +++ b/_includes/_help/videos/_posts/personalization.md @@ -3,6 +3,6 @@ Note: {{ include.site }} Office Hours talk for March 26, 2019, by Kelly Lockhart
      - +
      diff --git a/_includes/_help/videos/_posts/welcome.md b/_includes/_help/videos/_posts/welcome.md index 914c34f4..93e3ed91 100644 --- a/_includes/_help/videos/_posts/welcome.md +++ b/_includes/_help/videos/_posts/welcome.md @@ -3,6 +3,6 @@
      - +
      diff --git a/_includes/about-left-nav.html b/_includes/about-left-nav.html index 700cbddf..2ff3e759 100644 --- a/_includes/about-left-nav.html +++ b/_includes/about-left-nav.html @@ -1,6 +1,6 @@ -