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Add new prefix: nasaosdr (#1298)
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PubMed: https://pubmed.ncbi.nlm.nih.gov/39558178/
Database:
https://osdr.nasa.gov/bio/repo/search?q=&data_source=cgene,alsda&data_type=study

This pull request addresses the following issue:
#1293

This resource re-labels existing entries from NASA's GeneLab (`ngl`)
resource with new identifier formats.

The main difference in identifier formats is the first few letters of
the identifier. 'GLDS' for the old GeneLab and 'OSD' for the new
Open Science Data Repository (OSDR). The numbers proceeded by the
letters remain consistent across the two formats.

Resolving an old identifier pattern with the old uri_format pattern from
GeneLab automatically redirects you to the corresponding page on the
OSDR.

---------

Co-authored-by: Ben Gyori <ben.gyori@gmail.com>
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@nagutm @bgyori
nagutm and bgyori authored Dec 19, 2024
1 parent 7f12a22 commit 88c771f
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248 changes: 248 additions & 0 deletions src/bioregistry/data/bioregistry.json
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Expand Up @@ -74590,6 +74590,254 @@
},
"name": "National Academic Research and Collaborations Information System"
},
"nasaosdr.biospecimen": {
"contact": {
"email": "sylvain.v.costes@nasa.gov",
"name": "Sylvain V Costes",
"orcid": "0000-0002-8542-2389"
},
"contributor": {
"email": "m.naguthana@hotmail.com",
"github": "nagutm",
"name": "Mufaddal Naguthanawala",
"orcid": "0009-0009-5240-7463"
},
"description": "Identifiers for biospecimens used in experiments that investigate biological and health responses of terrestrial life to spaceflight",
"example": "7943",
"github_request_issue": 1298,
"homepage": "https://www.nasa.gov/osdr",
"name": "NASA Open Science Data Repository Biospecimen",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gkae1116",
"pubmed": "39558178",
"title": "NASA open science data repository: open science for life in space",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://osdr.nasa.gov/bio/repo/data/biospecimens/$1"
},
"nasaosdr.experiment": {
"contact": {
"email": "sylvain.v.costes@nasa.gov",
"name": "Sylvain V Costes",
"orcid": "0000-0002-8542-2389"
},
"contributor": {
"email": "m.naguthana@hotmail.com",
"github": "nagutm",
"name": "Mufaddal Naguthanawala",
"orcid": "0009-0009-5240-7463"
},
"description": "Identifiers for space-related data from experiments that investigate biological and health responses of terrestrial life to spaceflight",
"example": "OS-27",
"github_request_issue": 1298,
"homepage": "https://www.nasa.gov/osdr",
"name": "NASA Open Science Data Repository Experiment",
"pattern": "^OS-\\d+$",
"publications": [
{
"doi": "10.1093/nar/gkae1116",
"pubmed": "39558178",
"title": "NASA open science data repository: open science for life in space",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://osdr.nasa.gov/bio/repo/data/experiments/$1"
},
"nasaosdr.hardware": {
"contact": {
"email": "sylvain.v.costes@nasa.gov",
"name": "Sylvain V Costes",
"orcid": "0000-0002-8542-2389"
},
"contributor": {
"email": "m.naguthana@hotmail.com",
"github": "nagutm",
"name": "Mufaddal Naguthanawala",
"orcid": "0009-0009-5240-7463"
},
"description": "Identifiers for hardware used in experiments that investigate biological and health responses of terrestrial life to spaceflight",
"example": "2011",
"github_request_issue": 1298,
"homepage": "https://www.nasa.gov/osdr",
"name": "NASA Open Science Data Repository Hardware",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gkae1116",
"pubmed": "39558178",
"title": "NASA open science data repository: open science for life in space",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://osdr.nasa.gov/bio/repo/data/hardware/$1"
},
"nasaosdr.mission": {
"contact": {
"email": "sylvain.v.costes@nasa.gov",
"name": "Sylvain V Costes",
"orcid": "0000-0002-8542-2389"
},
"contributor": {
"email": "m.naguthana@hotmail.com",
"github": "nagutm",
"name": "Mufaddal Naguthanawala",
"orcid": "0009-0009-5240-7463"
},
"description": "Identifiers for missions associated with experiments that investigate biological and health responses of terrestrial life to spaceflight",
"example": "ARCBedrest",
"example_extras": [
"STS-46",
"Bion 11"
],
"github_request_issue": 1298,
"homepage": "https://www.nasa.gov/osdr",
"name": "NASA Open Science Data Repository Mission",
"pattern": "^.+$",
"publications": [
{
"doi": "10.1093/nar/gkae1116",
"pubmed": "39558178",
"title": "NASA open science data repository: open science for life in space",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://osdr.nasa.gov/bio/repo/data/missions/$1"
},
"nasaosdr.payload": {
"contact": {
"email": "sylvain.v.costes@nasa.gov",
"name": "Sylvain V Costes",
"orcid": "0000-0002-8542-2389"
},
"contributor": {
"email": "m.naguthana@hotmail.com",
"github": "nagutm",
"name": "Mufaddal Naguthanawala",
"orcid": "0009-0009-5240-7463"
},
"description": "Identifiers for payloads associated with experiments that investigate biological and health responses of terrestrial life to spaceflight",
"example": "VEG-03D",
"example_extras": [
"NanoRacks-UF-Squids-1",
"PSE.02",
"HyperG2-SIMBA2"
],
"github_request_issue": 1298,
"homepage": "https://www.nasa.gov/osdr",
"name": "NASA Open Science Data Repository Payload",
"pattern": "^.+$",
"publications": [
{
"doi": "10.1093/nar/gkae1116",
"pubmed": "39558178",
"title": "NASA open science data repository: open science for life in space",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://osdr.nasa.gov/bio/repo/data/payloads/$1"
},
"nasaosdr.study": {
"comment": "NASA OSDR is NASA's new integrated life sciences data archive which encompasses NASA GeneLAB (ngl), their old database for omics data. The studies from ngl are relabelled with new identifier formats, thus this is curated as a new prefix",
"contact": {
"email": "sylvain.v.costes@nasa.gov",
"name": "Sylvain V Costes",
"orcid": "0000-0002-8542-2389"
},
"contributor": {
"email": "m.naguthana@hotmail.com",
"github": "nagutm",
"name": "Mufaddal Naguthanawala",
"orcid": "0009-0009-5240-7463"
},
"description": "Identifiers for space-related data from studies that investigate biological and health responses of terrestrial life to spaceflight",
"example": "OSD-678",
"github_request_issue": 1298,
"homepage": "https://www.nasa.gov/osdr",
"name": "NASA Open Science Data Repository Study",
"pattern": "^OSD-\\d+$",
"publications": [
{
"doi": "10.1093/nar/gkae1116",
"pubmed": "39558178",
"title": "NASA open science data repository: open science for life in space",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://osdr.nasa.gov/bio/repo/data/studies/$1"
},
"nasaosdr.subject": {
"contact": {
"email": "sylvain.v.costes@nasa.gov",
"name": "Sylvain V Costes",
"orcid": "0000-0002-8542-2389"
},
"contributor": {
"email": "m.naguthana@hotmail.com",
"github": "nagutm",
"name": "Mufaddal Naguthanawala",
"orcid": "0009-0009-5240-7463"
},
"description": "Identifiers for subjects of experiments that investigate biological and health responses of terrestrial life to spaceflight",
"example": "58",
"github_request_issue": 1298,
"homepage": "https://www.nasa.gov/osdr",
"name": "NASA Open Science Data Repository Subject",
"pattern": "^\\d+$",
"publications": [
{
"doi": "10.1093/nar/gkae1116",
"pubmed": "39558178",
"title": "NASA open science data repository: open science for life in space",
"year": 2024
}
],
"reviewer": {
"email": "b.gyori@northeastern.edu",
"github": "bgyori",
"name": "Benjamin M. Gyori",
"orcid": "0000-0001-9439-5346"
},
"uri_format": "https://osdr.nasa.gov/bio/repo/data/subjects/$1"
},
"nasc": {
"biocontext": {
"prefix": "NASC"
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1 change: 1 addition & 0 deletions src/bioregistry/data/curated_papers.tsv
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Expand Up @@ -100,6 +100,7 @@ pubmed relevant orcid date_curated relevancy_type pr_added notes
39553733 0 0009-0009-5240-7463 2024-12-11 irrelevant_other 1305
39554224 0 0009-0009-5240-7463 2024-12-11 irrelevant_other 1305
39558158 1 0009-0009-5240-7463 2024-12-09 new_publication 1299 Publication for gpcrdb
39558178 1 0009-0009-5240-7463 2024-12-07 new_prefix 1298 New database for NASA GeneLab (ngl) resource. Re-labels existing entries with new identifiers
39558183 1 0009-0009-5240-7463 2024-12-16 new_publication 1333 Publication for string
39558184 1 0009-0009-5240-7463 2024-12-09 new_publication 1299 Publication for genbank
39558187 1 0009-0009-5240-7463 2024-12-11 new_publication 1304 Publication for rgap
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