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Add prefix: celldive, separating it out from dsmz #1478

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Add prefix: celldive, separating it out from dsmz #1478

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8ad6d35
Add prefix: celldive
nagutm Mar 22, 2025
cbb5c1c
Remove prefix: dsmz
nagutm Mar 22, 2025
199f175
Add synonym: dsmz
nagutm Mar 22, 2025
8b9f3a9
Re-add dsmz
nagutm Mar 26, 2025
17dbeac
style fix
nagutm Mar 26, 2025
88180cc
Update contributor and remove dsmz synonym
nagutm Mar 28, 2025
dbdd51a
remove conflicting synonyms from dsmz
nagutm Mar 28, 2025
74f3e16
Add part_of relationship to celldive
nagutm Mar 29, 2025
6487b2f
Remove cellosaurus mapping from dsmz prefix
nagutm Apr 23, 2025
817ed16
Merge remote-tracking branch 'upstream/main' into celldive
nagutm Apr 23, 2025
c4a01d5
Merge branch 'main' into celldive
bgyori Apr 29, 2025
51e622d
Update description and add reviewer info
bgyori Apr 29, 2025
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78 changes: 29 additions & 49 deletions src/bioregistry/data/bioregistry.json
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Original file line number Diff line number Diff line change
Expand Up @@ -14087,6 +14087,35 @@
},
"uri_format": "https://www.cellbankaustralia.com/$1.html"
},
"celldive": {
"cellosaurus": {
"category": "Cell line databases/resources",
"homepage": "https://celldive.dsmz.de/",
"name": "DSMZ Tools for Diving into Cell Line Data",
"prefix": "DSMZCellDive",
"uri_format": "https://celldive.dsmz.de/celllines/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "CellDive provides identifiers for authenticated human and animal cell lines, serving as reference models in biomedical research. These cell lines are characterized by various data types, including RNA-seq transcriptome profiles and short tandem repeat (STR) profiles, which ensure reproducibility and reliability. The resource enables researchers to identify and compare cell lines based on molecular and genomic features, supporting applications in cancer research, drug screening, and disease modeling",
"example": "ACC-1",
"github_request_issue": 1454,
"homepage": "https://celldive.dsmz.de/",
"mappings": {
"cellosaurus": "DSMZCellDive"
},
"name": "CellDive",
"pattern": "^ACC-\\d+$",
"synonyms": [
"dsmz",
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"DSMZCellDive"
],
"uri_format": "https://www.dsmz.de/collection/catalogue/details/culture/$1"
},
"cellimage": {
"biocontext": {
"prefix": "CELLIMAGE"
Expand Down Expand Up @@ -30676,55 +30705,6 @@
"prefix": "P1930"
}
},
"dsmz": {
"cellosaurus": {

@cthoyt cthoyt Mar 22, 2025

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it looks like a lot of components got lost, please make sure they are restored. How did you do the rename exactly? When I have done this, I just change the prefix, add the old prefix to the synonym list, then run bioregistry lint

@nagutm nagutm Mar 24, 2025

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I made the following changes when I renamed it:

  • removed the re3data mapping which was not mapping to CellDive, but DSMZ in general
  • removed example_extras because only the identifiers with ACC- format were for cell lines. For example, DSM-2 is for Paenibacillus macquariensis subsp. macquariensis, PV-0998 is for Apple chlorotic leaf spot virus ACLSV, etc.
  • Updated the regex pattern to only include ACC which is what covers cell lines.

The other identifier formats that are not ACC are related to specific microorganisms which felt like it was out of the scope for the celldive prefix so I intentionally removed them. Should these be maintained under a separate prefix or is it better to maintain this as part of the celldive prefix?

@cthoyt cthoyt Mar 24, 2025

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ahh I see what is happening. so we should probably maintain a superset dsmz prefix that is a union of all of these different vocabularies, since in practice they are conflated all together (and the ACC-, PV-, etc. work as janky subspaces)

@nagutm nagutm Mar 26, 2025

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In that case I can modify this PR to just be about adding the celldive prefix and create a new PR that modifies the existing dsmz prefix accordingly.

"category": "Cell line databases/resources",
"homepage": "https://celldive.dsmz.de/",
"name": "DSMZ Tools for Diving into Cell Line Data",
"prefix": "DSMZCellDive",
"uri_format": "https://celldive.dsmz.de/celllines/$1"
},
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
"description": "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line",
"example": "ACC-1",
"example_extras": [
"DSM-2",
"RT-0753",
"PC-0754",
"AS-0753",
"PV-0998"
],
"homepage": "https://www.dsmz.de",
"mappings": {
"cellosaurus": "DSMZCellDive",
"re3data": "r3d100010219"
},
"name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen",
"pattern": "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$",
"re3data": {
"description": "The DSMZ is the most comprehensive biological resource center worldwide. Being one of the world's largest collections, the DSMZ currently comprises more than 73,700 items, including about 31,900 different bacterial and 6,600 fungal strains, 840 human and animal cell lines, 1,500 plant viruses and antisera, 700 bacteriophages and 19,000 different types of bacterial genomic DNA. All biological materials accepted in the DSMZ collection are subject to extensive quality control and physiological and molecular characterization by our central services. In addition, DSMZ provides an extensive documentation and detailed diagnostic information on the biological materials. The unprecedented diversity and quality management of its bioresources render the DSMZ an internationally renowned supplier for science, diagnostic laboratories, national reference centers, as well as industrial partners.",
"homepage": "https://www.dsmz.de/",
"name": "DSMZ",
"prefix": "r3d100010219",
"synonyms": [
"Deutsche Sammlung von Mikroorganismen und Zellkulturen",
"Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures",
"Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen"
],
"xrefs": {
"nif": "0000-10209"
}
},
"synonyms": [
"DSMZCellDive"
],
"uri_format": "https://www.dsmz.de/collection/catalogue/details/culture/$1"
},
"dso": {
"contact": {
"email": "evan@epatters.org",
Expand Down