New prefix: hubmap #1548
New prefix: hubmap #1548
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This is along the right lines, however, similar to a recent discussion on #1541, HubMAP has distinct identifiers for datasets (this is what is currently represented in the PR) and collections (e.g., https://portal.hubmapconsortium.org/browse/collection/4964d24bbc6668a72c4cbb5e0393a6bc). It further has identifiers for samples (https://portal.hubmapconsortium.org/browse/sample/00f48355642651571ebd665e9bdc52a1) and donors (https://portal.hubmapconsortium.org/browse/donor/9d0274af06926c405696a533c2fbaeb9). These should all be represented as distinct prefixes like hubmap.dataset, hubmap.collection, etc. (They also have identifiers for publications but that is for a very small set and obscure enough that it is probably not worth curating.)
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@nalikapalayoor above, I mentioned that we should add |
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In this case, I would consider the identifier appearing in the URL as the dataset ID (i.e., |
| "name": "Nalika Palayoor", | ||
| "orcid": "0009-0008-8406-631X" | ||
| }, | ||
| "description": "The samples subsection of HuBMAP provides metadata about individual tissue samples collected from donors, and are the downstream experimental datasets for scRNA sequencing. Each sample has a unique identifier that links it to donor information, anatomical source, and related datasets.", |
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This seems like the wrong description here. This should be about hubmap.donor.
| "description": "The samples subsection of HuBMAP provides metadata about individual tissue samples collected from donors, and are the downstream experimental datasets for scRNA sequencing. Each sample has a unique identifier that links it to donor information, anatomical source, and related datasets.", | ||
| "example": "a3bc9e6193c47998758ac9d9bf9ddbb6", | ||
| "github_request_issue": 1548, | ||
| "homepage": "https://portal.hubmapconsortium.org/search/samples", |
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Wrong homepage, this should be for hubmap.donor
| "year": 2025 | ||
| } | ||
| ], | ||
| "uri_format": "https://portal.hubmapconsortium.org/browse/sample/$1" |
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| "uri_format": "https://portal.hubmapconsortium.org/browse/sample/$1" | |
| "uri_format": "https://portal.hubmapconsortium.org/browse/donor/$1" |
…into hubmap 8000 Merge
| "hubmap.collection": { | ||
| "contact": { | ||
| "email": "katy@iu.edu", | ||
| "github": "https://github.com/cns-iu/katy", |
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Github handles shouldn't contain the URL prefix
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1548 +/- ##
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+ Coverage 42.51% 47.16% +4.64%
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Files 117 122 +5
Lines 8327 8876 +549
Branches 1963 1495 -468
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+ Hits 3540 4186 +646
+ Misses 4582 4434 -148
- Partials 205 256 +51 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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This PR curates a new prefix called hubmap. It is from the Human BioMolecular Atlas Program resource.
Website: https://hubmapconsortium.org/
Pubmed: https://pubmed.ncbi.nlm.nih.gov/40082611/