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20 hours ago •
greenelab
greenelab
Investigate which id/date/etc fields to use from ORCID API in `orcid.py`
Checks
- [X] I have searched the docs, existing issues, and existing discussions for answers first.
Link to your website repo
https://github.com/andrewsu/sulab.org
Version of Lab Website Template you are using
1.2.1
Description
TLDR: I think orcid.py should be updated to get the external-id from the first work-summary entry, not from the first doi in external-ids.external-id.
Observed/desired behavior
On https://andrewsu.github.io/sulab.org/members/andrew-su.html, I see the following citation
The citation points to the biorxiv preprint (note that CSHL is the publisher/journal). However, in my ORCID profile, the preprint is grouped with the published article at Bioinformatics, and it is that version of the article that I've listed as the "Preferred source".
Therefore, I would expect that the citation on my profile page would list "Bioinformatics" as the journal/publisher and the link would go to the journal website, not biorxiv.
My diagnosis
When orcid.py retrieves my ORCID profile from https://pub.orcid.org/v3.0/0000-0002-9859-4104/works, this is the XML for the article above:
XML snippet for article above
<activities:group>
<common:last-modified-date>2024-04-21T02:40:56.931Z</common:last-modified-date>
<common:external-ids>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1101/2021.04.15.440028</common:external-id-value>
<common:external-id-normalized transient="true">10.1101/2021.04.15.440028</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1101/2021.04.15.440028</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1093/bioinformatics/btac205</common:external-id-value>
<common:external-id-normalized transient="true">10.1093/bioinformatics/btac205</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1093/bioinformatics/btac205</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<work:work-summary put-code="111796297" path="/0000-0002-9859-4104/work/111796297" visibility="public" display-index="3">
<common:created-date>2022-04-21T09:36:24.476Z</common:created-date>
<common:last-modified-date>2024-04-21T02:40:56.931Z</common:last-modified-date>
<common:source>
<common:source-client-id>
<common:uri>https://orcid.org/client/0000-0001-9884-1913</common:uri>
<common:path>0000-0001-9884-1913</common:path>
<common:host>orcid.org</common:host>
</common:source-client-id>
<common:source-name>Crossref</common:source-name>
</common:source>
<work:title>
<common:title>Design and application of a knowledge network for automatic prioritization of drug mechanisms</common:title>
</work:title>
<common:external-ids>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1093/bioinformatics/btac205</common:external-id-value>
<common:external-id-normalized transient="true">10.1093/bioinformatics/btac205</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1093/bioinformatics/btac205</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<common:url>https://doi.org/10.1093/bioinformatics/btac205</common:url>
<work:type>journal-article</work:type>
<common:publication-date>
<common:year>2022</common:year>
<common:month>05</common:month>
<common:day>13</common:day>
</common:publication-date>
<work:journal-title>Bioinformatics</work:journal-title>
</work:work-summary>
<work:work-summary put-code="92294640" path="/0000-0002-9859-4104/work/92294640" visibility="public" display-index="0">
<common:created-date>2021-04-16T08:27:32.678Z</common:created-date>
<common:last-modified-date>2022-06-01T04:14:25.366Z</common:last-modified-date>
<common:source>
<common:source-client-id>
<common:uri>https://orcid.org/client/0000-0001-9884-1913</common:uri>
<common:path>0000-0001-9884-1913</common:path>
<common:host>orcid.org</common:host>
</common:source-client-id>
<common:source-name>Crossref</common:source-name>
</common:source>
<work:title>
<common:title>Design and application of a knowledge network for automatic prioritization of drug mechanisms</common:title>
</work:title>
<common:external-ids>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1101/2021.04.15.440028</common:external-id-value>
<common:external-id-normalized transient="true">10.1101/2021.04.15.440028</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1101/2021.04.15.440028</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<common:url>https://doi.org/10.1101/2021.04.15.440028</common:url>
<work:type>other</work:type>
<common:publication-date>
<common:year>2021</common:year>
<common:month>04</common:month>
<common:day>15</common:day>
</common:publication-date>
</work:work-summary>
<work:work-summary put-code="158033604" path="/0000-0002-9859-4104/work/158033604" visibility="public" display-index="-1">
<common:created-date>2024-04-19T22:48:31.846Z</common:created-date>
<common:last-modified-date>2024-04-19T22:48:31.846Z</common:last-modified-date>
<common:source>
<common:source-orcid>
<common:uri>https://orcid.org/0000-0002-9859-4104</common:uri>
<common:path>0000-0002-9859-4104</common:path>
<common:host>orcid.org</common:host>
</common:source-orcid>
<common:source-name>Andrew I. Su</common:source-name>
</common:source>
<work:title>
<common:title>Design and application of a knowledge network for automatic prioritization of drug mechanisms</common:title>
</work:title>
<common:external-ids>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1101/2021.04.15.440028</common:external-id-value>
<common:external-id-normalized transient="true">10.1101/2021.04.15.440028</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1101/2021.04.15.440028</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1093/bioinformatics/btac205</common:external-id-value>
<common:external-id-normalized transient="true">10.1093/bioinformatics/btac205</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1093/bioinformatics/btac205</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<common:url>https://doi.org/10.1101/2021.04.15.440028</common:url>
<work:type>other</work:type>
<common:publication-date>
<common:year>2021</common:year>
<common:month>04</common:month>
<common:day>15</common:day>
</common:publication-date>
</work:work-summary>
</activities:group>
Currently, the code gets the list of IDs from external-ids.external-id section, and I believe it takes the first entry with a external-id-type of doi -- in this case, 10.1101/2021.04.15.440028. Unfortunately, this section does not look like there is any indication of the "preferred source". However, it appears that in the work-summary entries are listed so that the "preferred source" is listed first -- 10.1093/bioinformatics/btac205 is first.
I checked this behavior against another entry in my profile where the biorxiv article is listed as primary. See details below.
ORCID screenshot and XML snippet where biorxiv is listed as "preferred source"
<activities:group>
<common:last-modified-date>2024-04-19T22:48:31.838Z</common:last-modified-date>
<common:external-ids>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1101/367599</common:external-id-value>
<common:external-id-normalized transient="true">10.1101/367599</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1101/367599</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1021/acs.jproteome.8b00166</common:external-id-value>
<common:external-id-normalized transient="true">10.1021/acs.jproteome.8b00166</common:external-id-normalized>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
<common:external-id>
<common:external-id-type>eid</common:external-id-type>
<common:external-id-value>2-s2.0-85050359010</common:external-id-value>
<common:external-id-normalized transient="true">2-s2.0-85050359010</common:external-id-normalized>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<work:work-summary put-code="46481891" path="/0000-0002-9859-4104/work/46481891" visibility="public" display-index="0">
<common:created-date>2018-07-11T19:50:03.575Z</common:created-date>
<common:last-modified-date>2022-05-27T03:15:05.789Z</common:last-modified-date>
<common:source>
<common:source-client-id>
<common:uri>https://orcid.org/client/0000-0001-9884-1913</common:uri>
<common:path>0000-0001-9884-1913</common:path>
<common:host>orcid.org</common:host>
</common:source-client-id>
<common:source-name>Crossref</common:source-name>
</common:source>
<work:title>
<common:title>Triflic acid treatment enables LC-MS/MS analysis of insoluble bacterial biomass</common:title>
</work:title>
<common:external-ids>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1101/367599</common:external-id-value>
<common:external-id-normalized transient="true">10.1101/367599</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1101/367599</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<common:url>https://doi.org/10.1101/367599</common:url>
<work:type>other</work:type>
<common:publication-date>
<common:year>2018</common:year>
<common:month>07</common:month>
<common:day>11</common:day>
</common:publication-date>
</work:work-summary>
<work:work-summary put-code="54674396" path="/0000-0002-9859-4104/work/54674396" visibility="public" display-index="0">
<common:created-date>2019-02-27T20:02:31.774Z</common:created-date>
<common:last-modified-date>2022-05-27T21:53:54.347Z</common:last-modified-date>
<common:source>
<common:source-client-id>
<common:uri>https://orcid.org/client/0000-0002-5982-8983</common:uri>
<common:path>0000-0002-5982-8983</common:path>
<common:host>orcid.org</common:host>
</common:source-client-id>
<common:source-name>Scopus - Elsevier</common:source-name>
<common:assertion-origin-orcid>
<common:uri>https://orcid.org/0000-0002-9859-4104</common:uri>
<common:path>0000-0002-9859-4104</common:path>
<common:host>orcid.org</common:host>
</common:assertion-origin-orcid>
<common:assertion-origin-name>Andrew I. Su</common:assertion-origin-name>
</common:source>
<work:title>
<common:title>Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass</common:title>
</work:title>
<common:external-ids>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1021/acs.jproteome.8b00166</common:external-id-value>
<common:external-id-normalized transient="true">10.1021/acs.jproteome.8b00166</common:external-id-normalized>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
<common:external-id>
<common:external-id-type>eid</common:external-id-type>
<common:external-id-value>2-s2.0-85050359010</common:external-id-value>
<common:external-id-normalized transient="true">2-s2.0-85050359010</common:external-id-normalized>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<common:url>http://www.scopus.com/inward/record.url?eid=2-s2.0-85050359010&partnerID=MN8TOARS</common:url>
<work:type>journal-article</work:type>
<common:publication-date>
<common:year>2018</common:year>
</common:publication-date>
<work:journal-title>Journal of Proteome Research</work:journal-title>
</work:work-summary>
<work:work-summary put-code="158033601" path="/0000-0002-9859-4104/work/158033601" visibility="public" display-index="-1">
<common:created-date>2024-04-19T22:48:31.838Z</common:created-date>
<common:last-modified-date>2024-04-19T22:48:31.838Z</common:last-modified-date>
<common:source>
<common:source-orcid>
<common:uri>https://orcid.org/0000-0002-9859-4104</common:uri>
<common:path>0000-0002-9859-4104</common:path>
<common:host>orcid.org</common:host>
</common:source-orcid>
<common:source-name>Andrew I. Su</common:source-name>
</common:source>
<work:title>
<common:title>Triflic acid treatment enables LC-MS/MS analysis of insoluble bacterial biomass</common:title>
</work:title>
<common:external-ids>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1101/367599</common:external-id-value>
<common:external-id-normalized transient="true">10.1101/367599</common:external-id-normalized>
<common:external-id-url>https://doi.org/10.1101/367599</common:external-id-url>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
<common:external-id>
<common:external-id-type>doi</common:external-id-type>
<common:external-id-value>10.1021/acs.jproteome.8b00166</common:external-id-value>
<common:external-id-normalized transient="true">10.1021/acs.jproteome.8b00166</common:external-id-normalized>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
<common:external-id>
<common:external-id-type>eid</common:external-id-type>
<common:external-id-value>2-s2.0-85050359010</common:external-id-value>
<common:external-id-normalized transient="true">2-s2.0-85050359010</common:external-id-normalized>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<common:url>https://doi.org/10.1101/367599</common:url>
<work:type>other</work:type>
<common:publication-date>
<common:year>2018</common:year>
<common:month>07</common:month>
<common:day>11</common:day>
</common:publication-date>
</work:work-summary>
</activities:group>
Note that 10.1101/367599 is listed in the first work-summary section.
Based on all this, I think orcid.py should be updated to get the external-id from the first work-summary entry, not from the first doi in external-ids.external-id.
I'll look into this in depth later but off the bat I'll say that figuring out which fields to use was very difficult. I wasn't able to find any documentation on what fields meant what or which ones I should use. And in testing with Casey Greene's large listing I found that sometimes one field was the canonical paper and sometimes another one was. So, I'm not sure it's even consistent enough to always use one field or the other.
If I recall (I'm responding on mobile right now), I have it look all the way through one section of the response for a doi, then move on to another? Maybe it needs to check the first entry in one section, then the first entry in another, then back to the first section, and so on.
But this does feel like a situation where fixing it for you would break it for someone else. I'm not sure how to handle it.
You should be able to modify your orcid.py script to do what you want in the meantime. I might actually try to rope in a developer from orcid to tell me which fields to use.
After reading your reply, I realized I had a slight misconception about how the plugin worked. That means a potential enhancement might be easier to make than I was anticipating. Let me play around with it a bit -- I'll post here with more details. So no need for you to look at this more for the moment... Thanks for the quick reply!
So after closer look, the orcid plugin already gets IDs from the group.external-ids.external-id section and the group.work-summary.external-ids.external-id section, in that order. However, as documented above, the ordering in the group.work-summary.external-ids.external-id appears to better reflect the user intent (as people have curated their ORCID profile) than the group.external-ids.external-id section. So in my local version (git diff pasted below), I just reversed the priority order between those two sections. I also added a filter on external-id-relationship, requiring that to be "self". (When that value is "version-of" or "part-of", then those external-ids are less appropriate.)
To test this, I compared the IDs returned by both the current orcid.py and my local orcid.py for both my ORCID profile and Casey's ORCID profile. The list of IDs retrieved for me had differences in 7 out of 145 sources -- in all cases the local version returned IDs that reflected the "preferred source" in my ORCID profile (the journal version, not the biorxiv version), which to me is the desired behavior.
| current orcid.py | new orcid.py |
|---|---|
| id: doi:10.1101/2021.04.15.440028 | id: doi:10.1093/bioinformatics/btac205 |
| id: doi:10.1101/2020.04.05.026336 | id: doi:10.1186/s12915-020-00940-y |
| id: doi:10.15346/hc.v6i1.105 | id: doi:10.15346/hc.v6i1.4 |
| id: doi:10.1101/289371 | id: doi:10.1038/s41746-018-0052-2 |
| id: doi:10.1101/038083 | id: doi:10.5334/cstp.56 |
| id: doi:10.1101/032144 | id: doi:10.1093/database/baw015 |
| id: doi:10.1101/008383 | id: doi:10.1093/bioinformatics/btv061 |
The list of IDs retrieved for Casey's ORCID profile was exactly the same between both versions of the plugin code. So why does this affect me but not Casey? At least in a couple cases I looked at, Casey has separate entries for the journal paper and the biorxiv preprint. For example:
- Reproducibility of computational workflows is automated using continuous analysis
- biorxiv: doi:10.1101/056473
- journal: doi:10.1038/nbt.3780
- Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification
- biorxiv: doi:10.1101/039800
- journal: doi:10.1016/j.jbi.2016.10.007
You can also see these as separate entries on https://greenelab.com/members/casey-greene.html. Of course, it's possible and reasonable that Casey (and others) prefer to have the preprints and the journal articles as separate entries.
So to wrap up, I'm happy to create a PR if you think this change is useful to make to the template (or feel free to just make the commit yourself). Or, I'm happy to leave this as a local change on my instance and close this issue, and at least the solution is here to find if anyone needs it in the future. Your call, Vince!
$ git diff _cite/plugins/orcid.py
diff --git a/_cite/plugins/orcid.py b/_cite/plugins/orcid.py
index 0017145..333821b 100644
--- a/_cite/plugins/orcid.py
+++ b/_cite/plugins/orcid.py
@@ -35,13 +35,14 @@ def main(entry):
# go through response structure and pull out ids e.g. doi:1234/56789
for work in response:
# get list of ids
- ids = get_safe(work, "external-ids.external-id", [])
+ ids = []
for summary in get_safe(work, "work-summary", []):
ids = ids + get_safe(summary, "external-ids.external-id", [])
+ ids = ids + get_safe(work, "external-ids.external-id", [])
# prefer doi id type, or fallback to first id
_id = next(
- (id for id in ids if get_safe(id, "external-id-type", "") == "doi"),
+ (id for id in ids if get_safe(id, "external-id-type", "") == "doi" and get_safe(id, "external-id-relationship", "") == "self"),
ids[0] if len(ids) > 0 else {},
)
(Commit in https://github.com/andrewsu/sulab.org/commit/a0c70014c89dad40afc511366ec017abed1b69c4)
Thanks for your detailed research and comments on this.
I think this is worth keeping open and investigating more. I'd definitely like to get an authoritative answer on which field to use. I will sit down and look through this next week.
But for now yes please use your modification for your case.
I try to go into the publications list and change the preprint entry to a publication entry when it fails, but I am not always successful in remembering to do this.
@cgreene Do you have any contacts at ORCID that we could pull into this issue?
Just getting to this now. Still working on it. Some notes:
- ORCID doesn't really have support for technical implementations, so I didn't even bother filling out an official ticket.
- So, I'm going to ask for help on their public forum, but the response rate there doesn't look too good.
-
Here is the "documentation" for the
/worksendpoint (very insufficient). Many fields missing or uncommented. - Here's a docs page I eventually stumbled upon. A little bit better, but still doesn't tell us what we need to know.
I've asked to join that forum Google Group. Once I get access, I'll post a question about whether the works summary always should be preferred over the top level of the response. Intuitively, I would've expected the top level to be the "main" thing to look at, but 🤷. I don't feel the chances of getting a definitive or timely answer from the forums are high, so I may just make this change and hope that your case is representative. I'll also do my own check of Casey's corpus to make sure nothing gets screwed up there.
With this change I'm making in v1.2.2, I think I don't need to prioritize doi ID types anymore, and I can just look at whichever id is first. This will make it use Manubot in all but the most obscure cases. Let me know if you have thoughts on this. This might change some of your citations, as more of them will be generated via Manubot vs. ORCID. If you ever wanted to always keep the citation details ORCID returns, I believe it'd be as simple as removing the if id_type not in list... condition.
I also added a filter on external-id-relationship, requiring that to be "self".
~I just wish I could get information on what this field really means, beyond "external-id-relationship indicates the relationship between the item and the identifier". I may add this... I'll test it with Casey's corpus to see if it changes things too much. Do you have more info on this? Were you seeing "version of" for preprints, for example?~
Nevermind, it's explained here.
With this change I'm making in v1.2.2, I think I don't need to prioritize doi ID types anymore, and I can just look at whichever id is first. This will make it use Manubot in all but the most https://github.com/manubot/manubot/issues/365. Let me know if you have thoughts on this. This might change some of your citations, as more of them will be generated via Manubot vs. ORCID. If you ever wanted to always keep the citation details ORCID returns, I believe it'd be as simple as removing the if id_type not in list... condition.
I don't think this change will affect me much at all, since 98% of my citations use a doi prefix. (Much of the work in cleaning up my ORCID profile is merging non-doi IDs into the doi entries, which I consider to be the canonical ID.) If anything, I think it will help because manubot I'm guessing will not have ambiguous dates (between created-date and last-modified-date, for example), fixing the issue I raised in #260.
Here is a spreadsheet of a test I just did between the changes in v1.2.2 vs. the current implementation in v1.2.1, for both Andrew and Casey, with differences between old/new highlighted in red. I'm not seeing any differences for Casey, and quite a few for Andrew. I'm assuming that's because he seems to curate his preferred IDs for in his ORCID, and many of them are not DOIs.
Not sure what to make of this yet. The changes are "live" on the v1.2.2 branch, but need to think over this more.
Would you consider making this change as well? https://github.com/SuLab/sulab.org/commit/a0c70014c89dad40afc511366ec017abed1b69c4
I could be turned around here, but I think that would change it back so the vast majority of my IDs are DOIs, and it would not affect Casey's profile much or at all.
Wouldn't this make it so that the "preferred source" might not be selected? Like if you set your preferred to a PMID, will ORCID still fill in a DOI for the same source...
I think prioritizing the order over citation type might be the more correct thing to do, even if it changes things. I neglected to record the full citation details in that spreadshee, to see if Manubot still gave the same details between a doi and equivalent other id. I'll run the test again later and compare.
Wouldn't this make it so that the "preferred source" might not be selected? Like if you set your preferred to a PMID, will ORCID still fill in a DOI for the same source...
No, I don't think that's the case. I previously set all of my ORCID pubs so that the journal DOI was used for the "preferred source". I just flipped one entitled "Metaproteomics of colonic microbiota unveils discrete protein functions among colitic mice and control groups" so that the biorxiv DOI is preferred. So in my ORCID API XML , it is that work (and only that work) that has the biorxiv DOI (with prefix doi:10.1101) listed first in the work_summary section...
Okay Andrew, I've set up the following comparison with your ORCID.
Go to https://www.jsondiff.com/, open the browser dev console and paste this code:
compare script
let oldCitations = [
{
id: "doi:10.4049/jimmunol.2300769",
title:
"Repositioning the Early Pathology of Type 1 Diabetes to the Extraislet Vasculature",
authors: [
"Anne Costanzo",
"Don Clarke",
"Marie Holt",
"Siddhartha Sharma",
"Kenna Nagy",
"Xuqian Tan",
"Lisa Kain",
"Brian Abe",
"Sandrine Luce",
"Christian Boitard",
"Tine Wyseure",
"Laurent O. Mosnier",
"Andrew I. Su",
"Catherine Grimes",
"M. G. Finn",
"Paul B. Savage",
"Michael Gottschalk",
"Jeremy Pettus",
"Luc Teyton",
],
publisher: "The Journal of Immunology",
date: "2024-03-01",
link: "https://doi.org/gtr8pk",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1186/s12915-023-01764-2",
title:
"Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses",
authors: [
"Andra Waagmeester",
"Egon L. Willighagen",
"Andrew I. Su",
"Martina Kutmon",
"Jose Emilio Labra Gayo",
"Daniel Fernández-Álvarez",
"Quentin Groom",
"Peter J. Schaap",
"Lisa M. Verhagen",
"Jasper J. Koehorst",
],
publisher: "BMC Biology",
date: "2023-11-16",
link: "https://doi.org/gtrgz9",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1038/s41597-023-02534-z",
title: "DrugMechDB: A Curated Database of Drug Mechanisms",
authors: [
"Adriana Carolina Gonzalez-Cavazos",
"Anna Tanska",
"Michael Mayers",
"Denise Carvalho-Silva",
"Brindha Sridharan",
"Patrick A. Rewers",
"Umasri Sankarlal",
"Lakshmanan Jagannathan",
"Andrew I. Su",
],
publisher: "Scientific Data",
date: "2023-09-16",
link: "https://doi.org/gtrg2b",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1017/cts.2023.619",
title:
"An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges",
authors: [
"Karamarie Fecho",
"Chris Bizon",
"Tursynay Issabekova",
"Sierra Moxon",
"Anne E. Thessen",
"Shervin Abdollahi",
"Sergio E. Baranzini",
"Basazin Belhu",
"William E. Byrd",
"Lawrence Chung",
"Andrew Crouse",
"Marc P. Duby",
"Stephen Ferguson",
"Aleksandra Foksinska",
"Laura Forero",
"Jennifer Friedman",
"Vicki Gardner",
"Gwênlyn Glusman",
"Jennifer Hadlock",
"Kristina Hanspers",
"Eugene Hinderer",
"Charlotte Hobbs",
"Gregory Hyde",
"Sui Huang",
"David Koslicki",
"Philip Mease",
"Sandrine Muller",
"Christopher J. Mungall",
"Stephen A. Ramsey",
"Jared Roach",
"Irit Rubin",
"Shepherd H. Schurman",
"Anath Shalev",
"Brett Smith",
"Karthik Soman",
"Sarah Stemann",
"Andrew I. Su",
"Casey Ta",
"Paul B. Watkins",
"Mark D. Williams",
"Chunlei Wu",
"Colleen H. Xu",
],
publisher: "Journal of Clinical and Translational Science",
date: "2023-01-01",
link: "https://doi.org/gtr8pm",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1093/bioinformatics/btad570",
title:
"BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs",
authors: [
"Jackson Callaghan",
"Colleen H Xu",
"Jiwen Xin",
"Marco Alvarado Cano",
"Anders Riutta",
"Eric Zhou",
"Rohan Juneja",
"Yao Yao",
"Madhumita Narayan",
"Kristina Hanspers",
"Ayushi Agrawal",
"Alexander R Pico",
"Chunlei Wu",
"Andrew I Su",
],
publisher: "Bioinformatics",
date: "2023-09-01",
link: "https://doi.org/gtrg2c",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1186/s13195-023-01255-0",
title:
"Association study between drug prescriptions and Alzheimer’s disease claims in a commercial insurance database",
authors: ["Eric Hu", "Tong Shu Li", "Nathan E. Wineinger", "Andrew I. Su"],
publisher: "Alzheimer's Research & Therapy",
date: "2023-06-24",
link: "https://doi.org/gtr8pn",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1101/2023.05.12.540594",
title:
"Drug Repositioning using Consilience of Knowledge Graph Completion Methods",
authors: [
"Roger Tu",
"Meghamala Sinha",
"Carolina González",
"Eric Hu",
"Shehzaad Dhuliawala",
"Andrew McCallum",
"Andrew I. Su",
],
publisher: "Cold Spring Harbor Laboratory",
date: "2023-05-14",
link: "https://doi.org/gtrg2d",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1186/s12859-023-05258-4",
title:
"Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data",
authors: [
"Marco A. Cano",
"Ginger Tsueng",
"Xinghua Zhou",
"Jiwen Xin",
"Laura D. Hughes",
"Julia L. Mullen",
"Andrew I. Su",
"Chunlei Wu",
],
publisher: "BMC Bioinformatics",
date: "2023-04-20",
link: "https://doi.org/gr9ccd",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1038/s41597-023-01969-8",
title: "Addressing barriers in FAIR data practices for biomedical data",
authors: [
"Laura D. Hughes",
"Ginger Tsueng",
"Jack DiGiovanna",
"Thomas D. Horvath",
"Luke V. Rasmussen",
"Tor C. Savidge",
"Thomas Stoeger",
"Serdar Turkarslan",
"Qinglong Wu",
"Chunlei Wu",
"Andrew I. Su",
"Lars Pache",
],
publisher: "Scientific Data",
date: "2023-02-23",
link: "https://doi.org/gtr8pp",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1038/s41597-023-01968-9",
title:
"Developing a standardized but extendable framework to increase the findability of infectious disease datasets",
authors: [
"Ginger Tsueng",
"Marco A. Alvarado Cano",
"José Bento",
"Candice Czech",
"Mengjia Kang",
"Lars Pache",
"Luke V. Rasmussen",
"Tor C. Savidge",
"Justin Starren",
"Qinglong Wu",
"Jiwen Xin",
"Michael R. Yeaman",
"Xinghua Zhou",
"Andrew I. Su",
"Chunlei Wu",
"Liliana Brown",
"Reed S. Shabman",
"Laura D. Hughes",
"Serdar Turkarslan",
],
publisher: "Scientific Data",
date: "2023-02-23",
link: "https://doi.org/gtr8pq",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1038/s41592-023-01770-w",
title:
"Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources",
authors: [
"Ginger Tsueng",
"Julia L. Mullen",
"Manar Alkuzweny",
"Marco Cano",
"Benjamin Rush",
"Emily Haag",
"Jason Lin",
"Dylan J. Welzel",
"Xinghua Zhou",
"Zhongchao Qian",
"Alaa Abdel Latif",
"Emory Hufbauer",
"Mark Zeller",
"Kristian G. Andersen",
"Chunlei Wu",
"Andrew I. Su",
"Karthik Gangavarapu",
"Laura D. Hughes",
],
publisher: "Nature Methods",
date: "2023-02-23",
link: "https://doi.org/gtr8pr",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1038/s41592-023-01769-3",
title:
"Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations",
authors: [
"Karthik Gangavarapu",
"Alaa Abdel Latif",
"Julia L. Mullen",
"Manar Alkuzweny",
"Emory Hufbauer",
"Ginger Tsueng",
"Emily Haag",
"Mark Zeller",
"Christine M. Aceves",
"Karina Zaiets",
"Marco Cano",
"Xinghua Zhou",
"Zhongchao Qian",
"Rachel Sattler",
"Nathaniel L. Matteson",
"Joshua I. Levy",
"Raphael T. C. Lee",
"Lucas Freitas",
"Sebastian Maurer-Stroh",
"Marc A. Suchard",
"Chunlei Wu",
"Andrew I. Su",
"Kristian G. Andersen",
"Laura D. Hughes",
],
publisher: "Nature Methods",
date: "2023-02-23",
link: "https://doi.org/gr9gvs",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1111/cts.13302",
title:
"Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science",
authors: [
"Deepak R. Unni",
"Sierra A. T. Moxon",
"Michael Bada",
"Matthew Brush",
"Richard Bruskiewich",
"J. Harry Caufield",
"Paul A. Clemons",
"Vlado Dancik",
"Michel Dumontier",
"Karamarie Fecho",
"Gustavo Glusman",
"Jennifer J. Hadlock",
"Nomi L. Harris",
"Arpita Joshi",
"Tim Putman",
"Guangrong Qin",
"Stephen A. Ramsey",
"Kent A. Shefchek",
"Harold Solbrig",
"Karthik Soman",
"Anne E. Thessen",
"Melissa A. Haendel",
"Chris Bizon",
"Christopher J. Mungall",
],
publisher: "Clinical and Translational Science",
date: "2022-06-06",
link: "https://doi.org/gq6hdn",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1111/cts.13301",
title: "Progress toward a universal biomedical data translator",
authors: [
"Karamarie Fecho",
"Anne E. Thessen",
"Sergio E. Baranzini",
"Chris Bizon",
"Jennifer J. Hadlock",
"Sui Huang",
"Ryan T. Roper",
"Noel Southall",
"Casey Ta",
"Paul B. Watkins",
"Mark D. Williams",
"Hao Xu",
"William Byrd",
"Vlado Dančík",
"Marc P. Duby",
"Michel Dumontier",
"Gustavo Glusman",
"Nomi L. Harris",
"Eugene W. Hinderer",
"Greg Hyde",
"Adam Johs",
"Andrew I. Su",
"Guangrong Qin",
"Qian Zhu",
],
publisher: "Clinical and Translational Science",
date: "2022-06-06",
link: "https://doi.org/gq6hdk",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1101/2021.04.15.440028",
title:
"Design and application of a knowledge network for automatic prioritization of drug mechanisms",
authors: [
"Michael Mayers",
"Roger Tu",
"Dylan Steinecke",
"Tong Shu Li",
"Núria Queralt-Rosinach",
"Andrew I. Su",
],
publisher: "Cold Spring Harbor Laboratory",
date: "2021-04-15",
link: "https://doi.org/gtrg2h",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/j.gene.2022.146534",
title:
"A retrospective evaluation of a decade of Gene Wiki Reviews and their impact",
authors: [
"Andre J. van Wijnen",
"Erica Golemis",
"Israel Hanukoglu",
"Stephen Kwok-Wing Tsui",
"Eric Hu",
"Sabah Ul-Hasan",
"Janet Joy",
"Andrew I. Su",
"Ginger Tsueng",
],
publisher: "Gene",
date: "2022-07-01",
link: "https://doi.org/gtr8pt",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1093/bioinformatics/btac017",
title:
"BioThings SDK: a toolkit for building high-performance data APIs in biomedical research",
authors: [
"Sebastien Lelong",
"Xinghua Zhou",
"Cyrus Afrasiabi",
"Zhongchao Qian",
"Marco Alvarado Cano",
"Ginger Tsueng",
"Jiwen Xin",
"Julia Mullen",
"Yao Yao",
"Ricardo Avila",
"Greg Taylor",
"Andrew I Su",
"Chunlei Wu",
],
publisher: "Bioinformatics",
date: "2022-01-10",
link: "https://doi.org/gqn66z",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/j.mcpro.2022.100197",
title:
"Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis",
authors: [
"Peter S. Thuy-Boun",
"Ana Y. Wang",
"Ana Crissien-Martinez",
"Janice H. Xu",
"Sandip Chatterjee",
"Gregory S. Stupp",
"Andrew I. Su",
"Walter J. Coyle",
"Dennis W. Wolan",
],
publisher: "Molecular & Cellular Proteomics",
date: "2022-03-01",
link: "https://doi.org/gtr736",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1101/2020.04.05.026336",
title: "A protocol for adding knowledge to Wikidata, a case report",
authors: [
"Andra Waagmeester",
"Egon L. Willighagen",
"Andrew I Su",
"Martina Kutmon",
"Jose Emilio Labra Gayo",
"Daniel Fernández-Álvarez",
"Quentin Groom",
"Peter J. Schaap",
"Lisa M. Verhagen",
"Jasper J. Koehorst",
],
publisher: "Cold Spring Harbor Laboratory",
date: "2020-04-07",
link: "https://doi.org/gjqfrz",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.3390/genes11111384",
title:
"Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer",
authors: [
"Justin Wang",
"Ingrid Vallee",
"Aditi Dutta",
"Yu Wang",
"Zhongying Mo",
"Ze Liu",
"Haissi Cui",
"Andrew I. Su",
"Xiang-Lei Yang",
],
publisher: "Genes",
date: "2020-11-22",
link: "https://doi.org/ghstqb",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1126/scitranslmed.aan7967",
title:
"Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity",
authors: [
"Kwang Il Lee",
"Ramya Gamini",
"Merissa Olmer",
"Yasunari Ikuta",
"Joe Hasei",
"Jihye Baek",
"Oscar Alvarez-Garcia",
"Shawn P. Grogan",
"Darryl D. D’Lima",
"Hiroshi Asahara",
"Andrew I. Su",
"Martin K. Lotz",
],
publisher: "Science Translational Medicine",
date: "2020-10-28",
link: "https://doi.org/gm32nd",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1038/s41586-020-2577-1",
title:
"Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing",
authors: [
"Laura Riva",
"Shuofeng Yuan",
"Xin Yin",
"Laura Martin-Sancho",
"Naoko Matsunaga",
"Lars Pache",
"Sebastian Burgstaller-Muehlbacher",
"Paul D. De Jesus",
"Peter Teriete",
"Mitchell V. Hull",
"Max W. Chang",
"Jasper Fuk-Woo Chan",
"Jianli Cao",
"Vincent Kwok-Man Poon",
"Kristina M. Herbert",
"Kuoyuan Cheng",
"Tu-Trinh H. Nguyen",
"Andrey Rubanov",
"Yuan Pu",
"Courtney Nguyen",
"Angela Choi",
"Raveen Rathnasinghe",
"Michael Schotsaert",
"Lisa Miorin",
"Marion Dejosez",
"Thomas P. Zwaka",
"Ko-Yung Sit",
"Luis Martinez-Sobrido",
"Wen-Chun Liu",
"Kris M. White",
"Mackenzie E. Chapman",
"Emma K. Lendy",
"Richard J. Glynne",
"Randy Albrecht",
"Eytan Ruppin",
"Andrew D. Mesecar",
"Jeffrey R. Johnson",
"Christopher Benner",
"Ren Sun",
"Peter G. Schultz",
"Andrew I. Su",
"Adolfo García-Sastre",
"Arnab K. Chatterjee",
"Kwok-Yung Yuen",
"Sumit K. Chanda",
],
publisher: "Nature",
date: "2020-07-24",
link: "https://doi.org/gg5zh8",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.7554/elife.52614",
title: "Wikidata as a knowledge graph for the life sciences",
authors: [
"Andra Waagmeester",
"Gregory Stupp",
"Sebastian Burgstaller-Muehlbacher",
"Benjamin M Good",
"Malachi Griffith",
"Obi L Griffith",
"Kristina Hanspers",
"Henning Hermjakob",
"Toby S Hudson",
"Kevin Hybiske",
"Sarah M Keating",
"Magnus Manske",
"Michael Mayers",
"Daniel Mietchen",
"Elvira Mitraka",
"Alexander R Pico",
"Timothy Putman",
"Anders Riutta",
"Nuria Queralt-Rosinach",
"Lynn M Schriml",
"Thomas Shafee",
"Denise Slenter",
"Ralf Stephan",
"Katherine Thornton",
"Ginger Tsueng",
"Roger Tu",
"Sabah Ul-Hasan",
"Egon Willighagen",
"Chunlei Wu",
"Andrew I Su",
],
publisher: "eLife",
date: "2020-03-17",
link: "https://doi.org/ggqqc6",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1093/bioinformatics/btz678",
title:
"Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts",
authors: [
"Ginger Tsueng",
"Max Nanis",
"Jennifer T Fouquier",
"Michael Mayers",
"Benjamin M Good",
"Andrew I Su",
],
publisher: "Bioinformatics",
date: "2019-09-03",
link: "https://doi.org/ghbhx7",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.3389/fgene.2019.01355",
title:
"Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas",
authors: [
"Kim M. Summers",
"Stephen J. Bush",
"Chunlei Wu",
"Andrew I. Su",
"Charity Muriuki",
"Emily L. Clark",
"Heather A. Finlayson",
"Lel Eory",
"Lindsey A. Waddell",
"Richard Talbot",
"Alan L. Archibald",
"David A. Hume",
],
publisher: "Frontiers in Genetics",
date: "2020-02-14",
link: "https://doi.org/gj7mh4",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1093/database/baaa015",
title: "Structured reviews for data and knowledge-driven research",
authors: [
"Núria Queralt-Rosinach",
"Gregory S Stupp",
"Tong Shu Li",
"Michael Mayers",
"Maureen E Hoatlin",
"Matthew Might",
"Benjamin M Good",
"Andrew I Su",
],
publisher: "Database",
date: "2020-01-01",
link: "https://doi.org/ggsdkj",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1186/s12859-019-3297-0",
title:
"Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network",
authors: [
"Michael Mayers",
"Tong Shu Li",
"Núria Queralt-Rosinach",
"Andrew I. Su",
],
publisher: "BMC Bioinformatics",
date: "2019-12-01",
link: "https://doi.org/ggpcsr",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1371/journal.pone.0222165",
title:
"Advancing computational biology and bioinformatics research through open innovation competitions",
authors: [
"Andrea Blasco",
"Michael G. Endres",
"Rinat A. Sergeev",
"Anup Jonchhe",
"N. J. Maximilian Macaluso",
"Rajiv Narayan",
"Ted Natoli",
"Jin H. Paik",
"Bryan Briney",
"Chunlei Wu",
"Andrew I. Su",
"Aravind Subramanian",
"Karim R. Lakhani",
],
publisher: "PLOS ONE",
date: "2019-09-27",
link: "https://doi.org/gtr8pv",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1126/sciimmunol.aaw6329",
title:
"Position β57 of I-A\n <sup>g7</sup>\n controls early anti-insulin responses in NOD mice, linking an MHC susceptibility allele to type 1 diabetes onset",
authors: [
"Louis Gioia",
"Marie Holt",
"Anne Costanzo",
"Siddhartha Sharma",
"Brian Abe",
"Lisa Kain",
"Maki Nakayama",
"Xiaoxiao Wan",
"Andrew Su",
"Clayton Mathews",
"Yi-Guang Chen",
"Emil Unanue",
"Luc Teyton",
],
publisher: "Science Immunology",
date: "2019-08-02",
link: "https://doi.org/gtrg2k",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
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id: "doi:10.1073/pnas.1606297113",
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id: "doi:10.1073/pnas.122359899",
title:
"Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice",
authors: [
"Andrew I. Su",
"Luca G. Guidotti",
"John Paul Pezacki",
"Francis V. Chisari",
"Peter G. Schultz",
],
publisher: "Proceedings of the National Academy of Sciences",
date: "2002-08-12",
link: "https://doi.org/fmp",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1073/pnas.202608199",
title:
"Genomic analysis of the host response to hepatitis C virus infection",
authors: [
"Andrew I. Su",
"John P. Pezacki",
"Lisa Wodicka",
"Amy D. Brideau",
"Lubica Supekova",
"Robert Thimme",
"Stefan Wieland",
"Jens Bukh",
"Robert H. Purcell",
"Peter G. Schultz",
"Francis V. Chisari",
],
publisher: "Proceedings of the National Academy of Sciences",
date: "2002-11-19",
link: "https://doi.org/fmf",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/S1074-5521(02)00174-6",
title: "Genomic Effects of Polyamide/DNA Interactions on mRNA Expression",
authors: [
"Lubica Supekova",
"John Paul Pezacki",
"Andrew I. Su",
"Colin J. Loweth",
"Rainer Riedl",
"Bernhard Geierstanger",
"Peter G. Schultz",
"David E. Wemmer",
],
publisher: "Chemistry & Biology",
date: "2002-07-01",
link: "https://doi.org/fmq",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1073/pnas.012025199",
title: "Large-scale analysis of the human and mouse transcriptomes",
authors: [
"Andrew I. Su",
"Michael P. Cooke",
"Keith A. Ching",
"Yaron Hakak",
"John R. Walker",
"Tim Wiltshire",
"Anthony P. Orth",
"Raquel G. Vega",
"Lisa M. Sapinoso",
"Aziz Moqrich",
"Ardem Patapoutian",
"Garret M. Hampton",
"Peter G. Schultz",
"John B. Hogenesch",
],
publisher: "Proceedings of the National Academy of Sciences",
date: "2002-03-19",
link: "https://doi.org/fm5",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:11606367",
title:
"Molecular classification of human carcinomas by use of gene expression signatures.",
authors: [
"A I Su",
"J B Welsh",
"L M Sapinoso",
"S G Kern",
"P Dimitrov",
"H Lapp",
"P G Schultz",
"S M Powell",
"C A Moskaluk",
"H F Frierson",
"G M Hampton",
],
publisher: "Cancer research",
date: "2022-05-23",
link: "http://europepmc.org/abstract/med/11606367",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:11507037",
title:
"Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer.",
authors: [
"J B Welsh",
"L M Sapinoso",
"A I Su",
"S G Kern",
"J Wang-Rodriguez",
"C A Moskaluk",
"H F Frierson",
"G M Hampton",
],
publisher: "Cancer research",
date: "2022-05-23",
link: "http://europepmc.org/abstract/med/11507037",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/S0092-8674(01)00467-6",
title:
"A Comparison of the Celera and Ensembl Predicted Gene Sets Reveals Little Overlap in Novel Genes",
authors: [
"John B. Hogenesch",
"Keith A. Ching",
"Serge Batalov",
"Andrew I. Su",
"John R. Walker",
"Yingyao Zhou",
"Steve A. Kay",
"Peter G. Schultz",
"Michael P. Cooke",
],
publisher: "Cell",
date: "2001-08-01",
link: "https://doi.org/fn6",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1073/pnas.041452598",
title:
"Destabilization of Ca<sup>2+</sup>-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type",
authors: [
"Gayathri Ratnaswamy",
"Mary E. Huff",
"Andrew I. Su",
"Severine Rion",
"Jeffery W. Kelly",
],
publisher: "Proceedings of the National Academy of Sciences",
date: "2001-02-20",
link: "https://doi.org/bxfbhw",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1002/1097-0134(20010201)42:2<279::AID-PROT150>3.0.CO;2-U",
title:
"Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation",
authors: [
"Andrew I. Su",
"David M. Lorber",
"G. Scott Weston",
"Walter A. Baase",
"Brian W. Matthews",
"Brian K. Shoichet",
],
publisher: "Proteins: Structure, Function, and Genetics",
date: "2000-01-01",
link: "https://doi.org/dkvcvj",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1021/jm010451+",
title:
"Synthesis and Biological Evaluation of Myoseverin Derivatives: Microtubule Assembly Inhibitors",
authors: [
"Young-Tae Chang",
"Sarah M. Wignall",
"Gustavo R. Rosania",
"Nathanael S. Gray",
"Sarah R. Hanson",
"Andrew I. Su",
"John Merlie,",
"Ho-Sang Moon",
"Sameep B. Sangankar",
"Omar Perez",
"Rebecca Heald",
"Peter G. Schultz",
],
publisher: "Journal of Medicinal Chemistry",
date: "2001-11-21",
link: "https://doi.org/fpg",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
];
let newCitations = [
{
id: "pmid:38426888",
title:
"Repositioning the Early Pathology of Type 1 Diabetes to the Extraislet Vasculature.",
authors: [
"Anne Costanzo",
"Don Clarke",
"Marie Holt",
"Siddhartha Sharma",
"Kenna Nagy",
"Xuqian Tan",
"Lisa Kain",
"Brian Abe",
"Sandrine Luce",
"Christian Boitard",
"Tine Wyseure",
"Laurent O Mosnier",
"Andrew I Su",
"Catherine Grimes",
"M G Finn",
"Paul B Savage",
"Michael Gottschalk",
"Jeremy Pettus",
"Luc Teyton",
],
publisher: "Journal of immunology (Baltimore, Md. : 1950)",
date: "2024-04-01",
link: "https://www.ncbi.nlm.nih.gov/pubmed/38426888",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1186/s12915-023-01764-2",
title:
"Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses",
authors: [
"Andra Waagmeester",
"Egon L. Willighagen",
"Andrew I. Su",
"Martina Kutmon",
"Jose Emilio Labra Gayo",
"Daniel Fernández-Álvarez",
"Quentin Groom",
"Peter J. Schaap",
"Lisa M. Verhagen",
"Jasper J. Koehorst",
],
publisher: "BMC Biology",
date: "2023-11-16",
link: "https://doi.org/gtrgz9",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1038/s41597-023-02534-z",
title: "DrugMechDB: A Curated Database of Drug Mechanisms",
authors: [
"Adriana Carolina Gonzalez-Cavazos",
"Anna Tanska",
"Michael Mayers",
"Denise Carvalho-Silva",
"Brindha Sridharan",
"Patrick A. Rewers",
"Umasri Sankarlal",
"Lakshmanan Jagannathan",
"Andrew I. Su",
],
publisher: "Scientific Data",
date: "2023-09-16",
link: "https://doi.org/gtrg2b",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:37900350",
title:
"An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges.",
authors: [
"Karamarie Fecho",
"Chris Bizon",
"Tursynay Issabekova",
"Sierra Moxon",
"Anne E Thessen",
"Shervin Abdollahi",
"Sergio E Baranzini",
"Basazin Belhu",
"William E Byrd",
"Lawrence Chung",
"Andrew Crouse",
"Marc P Duby",
"Stephen Ferguson",
"Aleksandra Foksinska",
"Laura Forero",
"Jennifer Friedman",
"Vicki Gardner",
"Gwênlyn Glusman",
"Jennifer Hadlock",
"Kristina Hanspers",
"Eugene Hinderer",
"Charlotte Hobbs",
"Gregory Hyde",
"Sui Huang",
"David Koslicki",
"Philip Mease",
"Sandrine Muller",
"Christopher J Mungall",
"Stephen A Ramsey",
"Jared Roach",
"Irit Rubin",
"Shepherd H Schurman",
"Anath Shalev",
"Brett Smith",
"Karthik Soman",
"Sarah Stemann",
"Andrew I Su",
"Casey Ta",
"Paul B Watkins",
"Mark D Williams",
"Chunlei Wu",
"Colleen H Xu",
],
publisher: "Journal of clinical and translational science",
date: "2023-09-14",
link: "https://www.ncbi.nlm.nih.gov/pubmed/37900350",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1093/bioinformatics/btad570",
title:
"BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs",
authors: [
"Jackson Callaghan",
"Colleen H Xu",
"Jiwen Xin",
"Marco Alvarado Cano",
"Anders Riutta",
"Eric Zhou",
"Rohan Juneja",
"Yao Yao",
"Madhumita Narayan",
"Kristina Hanspers",
"Ayushi Agrawal",
"Alexander R Pico",
"Chunlei Wu",
"Andrew I Su",
],
publisher: "Bioinformatics",
date: "2023-09-01",
link: "https://doi.org/gtrg2c",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:37355615",
title:
"Association study between drug prescriptions and Alzheimer's disease claims in a commercial insurance database.",
authors: ["Eric Hu", "Tong Shu Li", "Nathan E Wineinger", "Andrew I Su"],
publisher: "Alzheimer's research & therapy",
date: "2023-06-24",
link: "https://www.ncbi.nlm.nih.gov/pubmed/37355615",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1101/2023.05.12.540594",
title:
"Drug Repositioning using Consilience of Knowledge Graph Completion Methods",
authors: [
"Roger Tu",
"Meghamala Sinha",
"Carolina González",
"Eric Hu",
"Shehzaad Dhuliawala",
"Andrew McCallum",
"Andrew I. Su",
],
publisher: "Cold Spring Harbor Laboratory",
date: "2023-05-14",
link: "https://doi.org/gtrg2d",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1101/2021.09.02.458726",
title:
"Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data",
authors: [
"Marco Cano",
"Ginger Tsueng",
"Xinghua Zhou",
"Laura D. Hughes",
"Julia L. Mullen",
"Jiwen Xin",
"Andrew I. Su",
"Chunlei Wu",
],
publisher: "Cold Spring Harbor Laboratory",
date: "2021-09-03",
link: "https://doi.org/gtrg2g",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:36823198",
title: "Addressing barriers in FAIR data practices for biomedical data.",
authors: [
"Laura D Hughes",
"Ginger Tsueng",
"Jack DiGiovanna",
"Thomas D Horvath",
"Luke V Rasmussen",
"Tor C Savidge",
"Thomas Stoeger",
"Serdar Turkarslan",
"Qinglong Wu",
"Chunlei Wu",
"Andrew I Su",
"Lars Pache",
],
publisher: "Scientific data",
date: "2023-02-23",
link: "https://www.ncbi.nlm.nih.gov/pubmed/36823198",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:36823157",
title:
"Developing a standardized but extendable framework to increase the findability of infectious disease datasets.",
authors: [
"Ginger Tsueng",
"Marco A Alvarado Cano",
"José Bento",
"Candice Czech",
"Mengjia Kang",
"Lars Pache",
"Luke V Rasmussen",
"Tor C Savidge",
"Justin Starren",
"Qinglong Wu",
"Jiwen Xin",
"Michael R Yeaman",
"Xinghua Zhou",
"Andrew I Su",
"Chunlei Wu",
"Liliana Brown",
"Reed S Shabman",
"Laura D Hughes",
],
publisher: "Scientific data",
date: "2023-02-23",
link: "https://www.ncbi.nlm.nih.gov/pubmed/36823157",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:36823331",
title:
"Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources.",
authors: [
"Ginger Tsueng",
"Julia L Mullen",
"Manar Alkuzweny",
"Marco Cano",
"Benjamin Rush",
"Emily Haag",
"Jason Lin",
"Dylan J Welzel",
"Xinghua Zhou",
"Zhongchao Qian",
"Alaa Abdel Latif",
"Emory Hufbauer",
"Mark Zeller",
"Kristian G Andersen",
"Chunlei Wu",
"Andrew I Su",
"Karthik Gangavarapu",
"Laura D Hughes",
],
publisher: "Nature methods",
date: "2023-02-23",
link: "https://www.ncbi.nlm.nih.gov/pubmed/36823331",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:36823332",
title:
"Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.",
authors: [
"Karthik Gangavarapu",
"Alaa Abdel Latif",
"Julia L Mullen",
"Manar Alkuzweny",
"Emory Hufbauer",
"Ginger Tsueng",
"Emily Haag",
"Mark Zeller",
"Christine M Aceves",
"Karina Zaiets",
"Marco Cano",
"Xinghua Zhou",
"Zhongchao Qian",
"Rachel Sattler",
"Nathaniel L Matteson",
"Joshua I Levy",
"Raphael T C Lee",
"Lucas Freitas",
"Sebastian Maurer-Stroh",
"Marc A Suchard",
"Chunlei Wu",
"Andrew I Su",
"Kristian G Andersen",
"Laura D Hughes",
],
publisher: "Nature methods",
date: "2023-02-23",
link: "https://www.ncbi.nlm.nih.gov/pubmed/36823332",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:36125173",
title:
"Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.",
authors: [
"Deepak R Unni",
"Sierra A T Moxon",
"Michael Bada",
"Matthew Brush",
"Richard Bruskiewich",
"J Harry Caufield",
"Paul A Clemons",
"Vlado Dancik",
"Michel Dumontier",
"Karamarie Fecho",
"Gustavo Glusman",
"Jennifer J Hadlock",
"Nomi L Harris",
"Arpita Joshi",
"Tim Putman",
"Guangrong Qin",
"Stephen A Ramsey",
"Kent A Shefchek",
"Harold Solbrig",
"Karthik Soman",
"Anne E Thessen",
"Melissa A Haendel",
"Chris Bizon",
"Christopher J Mungall",
],
publisher: "Clinical and translational science",
date: "2022-06-06",
link: "https://www.ncbi.nlm.nih.gov/pubmed/36125173",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:35611543",
title: "Progress toward a universal biomedical data translator.",
authors: [
"Karamarie Fecho",
"Anne E Thessen",
"Sergio E Baranzini",
"Chris Bizon",
"Jennifer J Hadlock",
"Sui Huang",
"Ryan T Roper",
"Noel Southall",
"Casey Ta",
"Paul B Watkins",
"Mark D Williams",
"Hao Xu",
"William Byrd",
"Vlado Dančík",
"Marc P Duby",
"Michel Dumontier",
"Gustavo Glusman",
"Nomi L Harris",
"Eugene W Hinderer",
"Greg Hyde",
"Adam Johs",
"Andrew I Su",
"Guangrong Qin",
"Qian Zhu",
],
publisher: "Clinical and translational science",
date: "2022-05-25",
link: "https://www.ncbi.nlm.nih.gov/pubmed/35611543",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1093/bioinformatics/btac205",
title:
"Design and application of a knowledge network for automatic prioritization of drug mechanisms",
authors: [
"Michael Mayers",
"Roger Tu",
"Dylan Steinecke",
"Tong Shu Li",
"Núria Queralt-Rosinach",
"Andrew I Su",
],
publisher: "Bioinformatics",
date: "2022-04-06",
link: "https://doi.org/gptwsz",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:35525475",
title:
"A retrospective evaluation of a decade of Gene Wiki Reviews and their impact.",
authors: [
"Andre J van Wijnen",
"Erica Golemis",
"Israel Hanukoglu",
"Stephen Kwok-Wing Tsui",
"Eric Hu",
"Sabah Ul-Hasan",
"Janet Joy",
"Andrew I Su",
"Ginger Tsueng",
],
publisher: "Gene",
date: "2022-05-04",
link: "https://www.ncbi.nlm.nih.gov/pubmed/35525475",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:35020801",
title:
"BioThings SDK: a toolkit for building high-performance data APIs in biomedical research.",
authors: [
"Sebastien Lelong",
"Xinghua Zhou",
"Cyrus Afrasiabi",
"Zhongchao Qian",
"Marco Alvarado Cano",
"Ginger Tsueng",
"Jiwen Xin",
"Julia Mullen",
"Yao Yao",
"Ricardo Avila",
"Greg Taylor",
"Andrew I Su",
"Chunlei Wu",
],
publisher: "Bioinformatics (Oxford, England)",
date: "2022-03-28",
link: "https://www.ncbi.nlm.nih.gov/pubmed/35020801",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:35033677",
title:
"Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis.",
authors: [
"Peter S Thuy-Boun",
"Ana Y Wang",
"Ana Crissien-Martinez",
"Janice H Xu",
"Sandip Chatterjee",
"Gregory S Stupp",
"Andrew I Su",
"Walter J Coyle",
"Dennis W Wolan",
],
publisher: "Molecular & cellular proteomics : MCP",
date: "2022-01-13",
link: "https://www.ncbi.nlm.nih.gov/pubmed/35033677",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1186/s12915-020-00940-y",
title:
"A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses",
authors: [
"Andra Waagmeester",
"Egon L. Willighagen",
"Andrew I. Su",
"Martina Kutmon",
"Jose Emilio Labra Gayo",
"Daniel Fernández-Álvarez",
"Quentin Groom",
"Peter J. Schaap",
"Lisa M. Verhagen",
"Jasper J. Koehorst",
],
publisher: "BMC Biology",
date: "2021-01-22",
link: "https://doi.org/gndrg7",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.3390/genes11111384",
title:
"Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer",
authors: [
"Justin Wang",
"Ingrid Vallee",
"Aditi Dutta",
"Yu Wang",
"Zhongying Mo",
"Ze Liu",
"Haissi Cui",
"Andrew I. Su",
"Xiang-Lei Yang",
],
publisher: "Genes",
date: "2020-11-22",
link: "https://doi.org/ghstqb",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:33115953",
title:
"Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity.",
authors: [
"Kwang Il Lee",
"Ramya Gamini",
"Merissa Olmer",
"Yasunari Ikuta",
"Joe Hasei",
"Jihye Baek",
"Oscar Alvarez-Garcia",
"Shawn P Grogan",
"Darryl D D'Lima",
"Hiroshi Asahara",
"Andrew I Su",
"Martin K Lotz",
],
publisher: "Science translational medicine",
date: "2020-10-28",
link: "https://www.ncbi.nlm.nih.gov/pubmed/33115953",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:32707573",
title:
"Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing.",
authors: [
"Laura Riva",
"Shuofeng Yuan",
"Xin Yin",
"Laura Martin-Sancho",
"Naoko Matsunaga",
"Lars Pache",
"Sebastian Burgstaller-Muehlbacher",
"Paul D De Jesus",
"Peter Teriete",
"Mitchell V Hull",
"Max W Chang",
"Jasper Fuk-Woo Chan",
"Jianli Cao",
"Vincent Kwok-Man Poon",
"Kristina M Herbert",
"Kuoyuan Cheng",
"Tu-Trinh H Nguyen",
"Andrey Rubanov",
"Yuan Pu",
"Courtney Nguyen",
"Angela Choi",
"Raveen Rathnasinghe",
"Michael Schotsaert",
"Lisa Miorin",
"Marion Dejosez",
"Thomas P Zwaka",
"Ko-Yung Sit",
"Luis Martinez-Sobrido",
"Wen-Chun Liu",
"Kris M White",
"Mackenzie E Chapman",
"Emma K Lendy",
"Richard J Glynne",
"Randy Albrecht",
"Eytan Ruppin",
"Andrew D Mesecar",
"Jeffrey R Johnson",
"Christopher Benner",
"Ren Sun",
"Peter G Schultz",
"Andrew I Su",
"Adolfo García-Sastre",
"Arnab K Chatterjee",
"Kwok-Yung Yuen",
"Sumit K Chanda",
],
publisher: "Nature",
date: "2020-07-24",
link: "https://www.ncbi.nlm.nih.gov/pubmed/32707573",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
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link: "https://doi.org/fg3",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1101/gr.2161804",
title: "Applications of a Rat Multiple Tissue Gene Expression Data Set",
authors: [
"John R. Walker",
"Andrew I. Su",
"David W. Self",
"John B. Hogenesch",
"Hilmar Lapp",
"Rainer Maier",
"Daniel Hoyer",
"Graeme Bilbe",
],
publisher: "Genome Research",
date: "2004-04-01",
link: "https://doi.org/dcfv8j",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1371/journal.pbio.0020393",
title:
"Use of a Dense Single Nucleotide Polymorphism Map for In Silico Mapping in the Mouse",
authors: [
"Mathew T Pletcher",
"Philip McClurg",
"Serge Batalov",
"Andrew I Su",
"S. Whitney Barnes",
"Erica Lagler",
"Ron Korstanje",
"Xiaosong Wang",
"Deborah Nusskern",
"Molly A Bogue",
"Richard J Mural",
"Beverly Paigen",
"Tim Wiltshire",
],
publisher: "PLoS Biology",
date: "2004-11-09",
link: "https://doi.org/ff3",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/S1097-2765(03)00199-0",
title:
"Genome-Wide Analysis of CREB Target Genes Reveals A Core Promoter Requirement for cAMP Responsiveness",
authors: [
"Michael D Conkright",
"Ernesto Guzmán",
"Lawrence Flechner",
"Andrew I Su",
"John B Hogenesch",
"Marc Montminy",
],
publisher: "Molecular Cell",
date: "2003-05-01",
link: "https://doi.org/c3dzjj",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/S1097-2765(03)00134-5",
title:
"Genome-Wide Analysis of CREB Target Genes Reveals A Core Promoter Requirement for cAMP Responsiveness",
authors: [
"Michael D. Conkright",
"Ernesto Guzmán",
"Lawrence Flechner",
"Andrew I. Su",
"John B. Hogenesch",
"Marc Montminy",
],
publisher: "Molecular Cell",
date: "2003-04-01",
link: "https://doi.org/fkb",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:12368205",
title:
"Large scale molecular analysis identifies genes with altered expression in salivary adenoid cystic carcinoma.",
authors: [
"Henry F Frierson",
"Adel K El-Naggar",
"John B Welsh",
"Lisa M Sapinoso",
"Andrew I Su",
"Jun Cheng",
"Takashi Saku",
"Christopher A Moskaluk",
"Garret M Hampton",
],
publisher: "The American journal of pathology",
date: "2002-10-01",
link: "https://www.ncbi.nlm.nih.gov/pubmed/12368205",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/S0092-8674(02)00722-5",
title:
"Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock",
authors: [
"Satchidananda Panda",
"Marina P. Antoch",
"Brooke H. Miller",
"Andrew I. Su",
"Andrew B. Schook",
"Marty Straume",
"Peter G. Schultz",
"Steve A. Kay",
"Joseph S. Takahashi",
"John B. Hogenesch",
],
publisher: "Cell",
date: "2002-05-01",
link: "https://doi.org/fmz",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1073/pnas.122359899",
title:
"Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice",
authors: [
"Andrew I. Su",
"Luca G. Guidotti",
"John Paul Pezacki",
"Francis V. Chisari",
"Peter G. Schultz",
],
publisher: "Proceedings of the National Academy of Sciences",
date: "2002-08-12",
link: "https://doi.org/fmp",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1073/pnas.202608199",
title:
"Genomic analysis of the host response to hepatitis C virus infection",
authors: [
"Andrew I. Su",
"John P. Pezacki",
"Lisa Wodicka",
"Amy D. Brideau",
"Lubica Supekova",
"Robert Thimme",
"Stefan Wieland",
"Jens Bukh",
"Robert H. Purcell",
"Peter G. Schultz",
"Francis V. Chisari",
],
publisher: "Proceedings of the National Academy of Sciences",
date: "2002-11-19",
link: "https://doi.org/fmf",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/S1074-5521(02)00174-6",
title: "Genomic Effects of Polyamide/DNA Interactions on mRNA Expression",
authors: [
"Lubica Supekova",
"John Paul Pezacki",
"Andrew I. Su",
"Colin J. Loweth",
"Rainer Riedl",
"Bernhard Geierstanger",
"Peter G. Schultz",
"David E. Wemmer",
],
publisher: "Chemistry & Biology",
date: "2002-07-01",
link: "https://doi.org/fmq",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1073/pnas.012025199",
title: "Large-scale analysis of the human and mouse transcriptomes",
authors: [
"Andrew I. Su",
"Michael P. Cooke",
"Keith A. Ching",
"Yaron Hakak",
"John R. Walker",
"Tim Wiltshire",
"Anthony P. Orth",
"Raquel G. Vega",
"Lisa M. Sapinoso",
"Aziz Moqrich",
"Ardem Patapoutian",
"Garret M. Hampton",
"Peter G. Schultz",
"John B. Hogenesch",
],
publisher: "Proceedings of the National Academy of Sciences",
date: "2002-03-19",
link: "https://doi.org/fm5",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:11606367",
title:
"Molecular classification of human carcinomas by use of gene expression signatures.",
authors: [
"A I Su",
"J B Welsh",
"L M Sapinoso",
"S G Kern",
"P Dimitrov",
"H Lapp",
"P G Schultz",
"S M Powell",
"C A Moskaluk",
"H F Frierson",
"G M Hampton",
],
publisher: "Cancer research",
date: "2001-10-15",
link: "https://www.ncbi.nlm.nih.gov/pubmed/11606367",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "pmid:11507037",
title:
"Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer.",
authors: [
"J B Welsh",
"L M Sapinoso",
"A I Su",
"S G Kern",
"J Wang-Rodriguez",
"C A Moskaluk",
"H F Frierson",
"G M Hampton",
],
publisher: "Cancer research",
date: "2001-08-15",
link: "https://www.ncbi.nlm.nih.gov/pubmed/11507037",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1016/S0092-8674(01)00467-6",
title:
"A Comparison of the Celera and Ensembl Predicted Gene Sets Reveals Little Overlap in Novel Genes",
authors: [
"John B. Hogenesch",
"Keith A. Ching",
"Serge Batalov",
"Andrew I. Su",
"John R. Walker",
"Yingyao Zhou",
"Steve A. Kay",
"Peter G. Schultz",
"Michael P. Cooke",
],
publisher: "Cell",
date: "2001-08-01",
link: "https://doi.org/fn6",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1073/pnas.041452598",
title:
"Destabilization of Ca<sup>2+</sup>-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type",
authors: [
"Gayathri Ratnaswamy",
"Mary E. Huff",
"Andrew I. Su",
"Severine Rion",
"Jeffery W. Kelly",
],
publisher: "Proceedings of the National Academy of Sciences",
date: "2001-02-20",
link: "https://doi.org/bxfbhw",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1002/1097-0134(20010201)42:2<279::AID-PROT150>3.0.CO;2-U",
title:
"Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation",
authors: [
"Andrew I. Su",
"David M. Lorber",
"G. Scott Weston",
"Walter A. Baase",
"Brian W. Matthews",
"Brian K. Shoichet",
],
publisher: "Proteins: Structure, Function, and Genetics",
date: "2000-01-01",
link: "https://doi.org/dkvcvj",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
{
id: "doi:10.1021/jm010451+",
title:
"Synthesis and Biological Evaluation of Myoseverin Derivatives: Microtubule Assembly Inhibitors",
authors: [
"Young-Tae Chang",
"Sarah M. Wignall",
"Gustavo R. Rosania",
"Nathanael S. Gray",
"Sarah R. Hanson",
"Andrew I. Su",
"John Merlie,",
"Ho-Sang Moon",
"Sameep B. Sangankar",
"Omar Perez",
"Rebecca Heald",
"Peter G. Schultz",
],
publisher: "Journal of Medicinal Chemistry",
date: "2001-11-21",
link: "https://doi.org/fpg",
orcid: "0000-0002-9859-4104",
plugin: "orcid.py",
file: "orcid.yaml",
},
];
var script = document.createElement("script");
script.src = "https://www.unpkg.com/string-comparisons";
document.head.appendChild(script);
await new Promise((resolve) => (script.onload = resolve));
const matches = [];
for (const oldCitation of oldCitations)
for (const newCitation of newCitations) {
const oldTitle = oldCitation.title.toLowerCase().replace(/[^a-z]/, "");
const newTitle = newCitation.title.toLowerCase().replace(/[^a-z]/, "");
if (
oldTitle.includes(newTitle) ||
newTitle.includes(oldTitle) ||
Trigram.similarity(oldTitle, newTitle) > 0.9
)
matches.push([oldCitation, newCitation]);
}
for (const oldCitation of oldCitations)
if (!matches.find((match) => match[0] === oldCitation))
matches.push([oldCitation, null]);
for (const newCitation of newCitations)
if (!matches.find((match) => match[1] === newCitation))
matches.push([null, newCitation]);
oldCitations = matches.map((match) => match[0]);
newCitations = matches.map((match) => match[1]);
console.log(oldCitations, newCitations);
It should print two lists of citations, old (v1.2.1) vs. new (v1.2.2). If you're using Chrome, you can right click them to copy to clipboard and paste them into the diff tool.
Looking over the diff... the IDs are different of course, but the dates are also different. The titles and author names seem to be different but equivalent, just spot checking them. Here's a preview of the differences:
I'm not sure what to make of all of this. I feel like I want to change the behavior to not prefer DOIs, and instead prefer the first work summary, which seems to reflect the author's preferences the best. We only have Andrew's data point for this, but in absence of any documentation or support, it's the best we can do. I didn't analyze Casey's citation differences because his IDs didn't change; they're all basically DOIs in new and old.
@cgreene Do you have opinions on what the picking algo should be here? Summary: Currently, the orcid template plugin prefers DOI citations over any other type. (Don't know why I did this originally... Consistency? DOI's inherently "better"? Manubot could cite them "better"?). Now, just based on Andrew's case and no documentation, it seems like just picking the first ID from the orcid reflects what the author has selected as their "preferred source" on orcid.org. Not sure how this affects people who haven't set any preferred source.