Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add 63 new prefixes to support full Ooh Na Na database build #261

Merged
merged 62 commits into from
Dec 8, 2021
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
62 commits
Select commit Hold shift + click to select a range
d45b190
Update bioregistry.json
cthoyt Dec 1, 2021
2a98c53
Merge branch 'main' into updates-for-pyobo
cthoyt Dec 1, 2021
0c7ce3e
Update bioregistry.json
cthoyt Dec 1, 2021
7afa67e
Update bioregistry.json
cthoyt Dec 1, 2021
856ef7f
Update bioregistry.json
cthoyt Dec 1, 2021
7495cc7
Update bioregistry.json
cthoyt Dec 1, 2021
43ea80e
Update bioregistry.json
cthoyt Dec 1, 2021
c0cf56c
Update curation.tsv
cthoyt Dec 1, 2021
5b0e3f0
Skip cellosaurus entries with no format uri
cthoyt Dec 1, 2021
198a419
Update bioregistry.json
cthoyt Dec 1, 2021
20c84d5
Update cellosaurus.py
cthoyt Dec 1, 2021
30b3c25
Update utils.py
cthoyt Dec 1, 2021
da0a806
Update processed data
cthoyt Dec 1, 2021
984f1ca
Update bioregistry.json
cthoyt Dec 1, 2021
51f3b23
Update bioregistry.json
cthoyt Dec 1, 2021
cae440e
Update curation.tsv
cthoyt Dec 1, 2021
5631c82
Add back filtered missing URI formatter
cthoyt Dec 1, 2021
a3165b4
Update lincs link
cthoyt Dec 1, 2021
006a8dc
Update cellosaurus alignment
cthoyt Dec 1, 2021
19f909f
Update bioregistry.json
cthoyt Dec 1, 2021
7a1d7e4
Merge branch 'main' into updates-for-pyobo
cthoyt Dec 1, 2021
3173d16
Merge branch 'main' into updates-for-pyobo
cthoyt Dec 1, 2021
01c3bf9
Merge branch 'main' into updates-for-pyobo
cthoyt Dec 1, 2021
5013827
Update bioregistry.json
cthoyt Dec 1, 2021
277a0d6
Add NPO
cthoyt Dec 1, 2021
9ae306f
Add FTT (used in ENVO)
cthoyt Dec 1, 2021
7ac6562
Add GeoNames (used in ENVO)
cthoyt Dec 1, 2021
bfe1e65
Add GEMET (used in ENVO)
cthoyt Dec 1, 2021
394e929
Add LTER (used in ENVO)
cthoyt Dec 1, 2021
9be766d
Reformat
cthoyt Dec 1, 2021
7e118fa
Add CMECS (used in ENVO)
cthoyt Dec 1, 2021
e06dc84
Add ExoLexicon (used in ENVO)
cthoyt Dec 1, 2021
3b2c21e
Update bioregistry.json
cthoyt Dec 1, 2021
829abe7
Add SWEET Ontology (used in ENVO)
cthoyt Dec 1, 2021
33fed1d
Add synonym for WWF (for ENVO)
cthoyt Dec 1, 2021
ea7c17c
Update SABIO-RK for GO
cthoyt Dec 2, 2021
854e155
Update bioregistry.json
cthoyt Dec 2, 2021
41266aa
Add FlyBrain Neuron Database
cthoyt Dec 2, 2021
6996851
Add VSP (for MAXO)
cthoyt Dec 2, 2021
9f1e010
Add inhand (for HPATH)
cthoyt Dec 2, 2021
f7af6ff
Add synonym for HPATH
cthoyt Dec 2, 2021
73b0458
Add NCBI book (for MAXO)
cthoyt Dec 2, 2021
ec44570
Update curation.tsv
cthoyt Dec 2, 2021
189a9bb
Collapse cosmicclp inco cosmic.cell
cthoyt Dec 2, 2021
ed2b2cf
Add REO information
cthoyt Dec 2, 2021
b9a3a24
Merge cosmicclp and cosmic.cell
cthoyt Dec 2, 2021
9b445d0
Update NCRO downloads
cthoyt Dec 2, 2021
996c60b
Add GO Chemicals
cthoyt Dec 2, 2021
279ee93
Update bioregistry.json
cthoyt Dec 8, 2021
3276916
Update bioregistry.json
cthoyt Dec 8, 2021
b8a1c70
Add apaonto
cthoyt Dec 8, 2021
007db0a
Update bioregistry.json
cthoyt Dec 8, 2021
b60cfab
Merge branch 'main' into updates-for-pyobo
cthoyt Dec 8, 2021
852bcc5
Update getters.py
cthoyt Dec 8, 2021
2bc22dd
Add examples
cthoyt Dec 8, 2021
261ca93
Update bioregistry.json
cthoyt Dec 8, 2021
5c71fa1
Add remaining examples
cthoyt Dec 8, 2021
d4df0ca
Align bioportal
cthoyt Dec 8, 2021
cfa9b0f
Update bioregistry.json
cthoyt Dec 8, 2021
cecc4d8
Add homepages
cthoyt Dec 8, 2021
68628bb
Finish descriptions
cthoyt Dec 8, 2021
6dc4f30
Add missing contributor information
cthoyt Dec 8, 2021
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 0 additions & 2 deletions src/bioregistry/align/cellosaurus.py
Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,6 @@ class CellosaurusAligner(Aligner):
def get_skip(self) -> Mapping[str, str]:
"""Get the skipped Cellosaurus identifiers."""
return {
"Biosample": "",
"CCRID": "not in english",
"CCTCC": "dead site",
"CCLV": "stub website, URL dead",
}
Expand Down
4 changes: 2 additions & 2 deletions src/bioregistry/align/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from ..data import EXTERNAL
from ..resource_manager import Manager
from ..schema import Resource
from ..utils import is_mismatch, read_metaregistry
from ..utils import is_mismatch, norm, read_metaregistry

__all__ = [
"Aligner",
Expand Down Expand Up @@ -77,7 +77,7 @@ def _align(self):

# add the identifier from an external resource if it's been marked as high quality
if bioregistry_id is None and self.include_new:
bioregistry_id = external_id
bioregistry_id = norm(external_id)
self.internal_registry[bioregistry_id] = Resource()

if bioregistry_id is not None: # a match was found
Expand Down
Loading