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monarch-initiative
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omim
Data ingest pipeline for OMIM.
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SSSOM misc updates
#54
joeflack4
closed
2 years ago
0
Add `mapping_set_description` to `sssom.metadata.yml`
#53
joeflack4
closed
2 years ago
0
Review SSSOM metadata
#52
matentzn
closed
2 years ago
1
Pipenv -> pip || poetry||tox
#51
joeflack4
opened
2 years ago
1
Update equivalency predicates
#50
joeflack4
closed
1 year ago
0
Reconcile inconsistent HGNC mappings
#49
joeflack4
closed
2 years ago
3
HGNC-related updates & `skos:exactMatch` -> `oboInOwl:hasExactSynonym`
#48
joeflack4
closed
2 years ago
1
Get HGNC IDs in addition to symbols
#47
joeflack4
closed
2 years ago
1
Create a complete UMLS-OMIM SSSOM mapping file
#46
matentzn
closed
2 years ago
4
OMIM gene equivalencies cause cycles/cliques
#45
matentzn
closed
2 years ago
16
Create a complete HGNC-OMIM SSSOM mapping file
#44
matentzn
closed
2 years ago
6
Difference with the official OMIM
#43
Lawhy
opened
2 years ago
7
URI with http or https
#42
hrshdhgd
closed
1 year ago
2
Ingest uses skos:exactMatch instead of oboInOwl:hasExactSynonym
#41
matentzn
closed
2 years ago
2
OMIM releases should be versioned moving forward
#40
matentzn
opened
2 years ago
1
Several updates
#39
joeflack4
closed
2 years ago
0
Cant run release myself
#38
matentzn
closed
2 years ago
1
OMIMPS URL should be https://www.omim.org/phenotypicSeries/PS
#37
matentzn
closed
2 years ago
5
omim.owl in the release should be called omim.owl
#36
matentzn
closed
1 year ago
1
hasSynonymType needs to be declared an OWL annotation property
#35
matentzn
closed
2 years ago
4
Not enough terms labeled w/ `biolink:category biolink:Disease`?
#34
joeflack4
closed
2 years ago
3
OMIM alternative title should be exact synonyms
#33
nicolevasilevsky
closed
2 years ago
0
Utilize titles from `morbidMap.txt` in addition to `mimTitles.txt`
#32
joeflack4
opened
2 years ago
0
Finish automation & add a GitHub Action
#31
joeflack4
opened
2 years ago
6
Tag annotations such as synonyms and definitions with the data model entry they come from
#30
matentzn
opened
2 years ago
0
Delete data/omim.ttl
#29
matentzn
closed
1 year ago
1
OMIM synonym scope needs review
#28
joeflack4
opened
2 years ago
2
OMIM synonyms should be broken into synonyms - main term and abbreviation
#27
joeflack4
closed
2 years ago
1
Super-issue: Capitalization
#26
joeflack4
opened
2 years ago
0
Typos in capitalization
#25
joeflack4
opened
2 years ago
0
OMIM slurp: dna should be capitalized (DNA)
#24
nicolevasilevsky
opened
2 years ago
0
OMIM slurp: If a letter follows a number, it should be capitalized
#23
nicolevasilevsky
opened
2 years ago
0
Acronyms should get ABBREVIATION tag
#22
matentzn
opened
2 years ago
0
Synonyms should be "exact" by default, not "related"
#21
matentzn
opened
2 years ago
0
Create GitHub action that runs scraping once per week
#20
matentzn
opened
2 years ago
1
Combine 'fetch PMIDs' and 'web scrape new codes' w/ overall pipeline
#19
joeflack4
closed
2 years ago
1
Auto generate 'latest release' on PR merge
#18
joeflack4
opened
3 years ago
2
Test: Output should be processable by ROBOT
#17
joeflack4
closed
2 years ago
1
Changed so that BNodes have a deterministic ID
#16
joeflack4
closed
3 years ago
2
Build should be deterministic
#15
joeflack4
closed
3 years ago
0
Repo should be public, no need to hide :)
#14
matentzn
closed
2 years ago
7
Makefile addition and minor updates / bugfixes
#13
joeflack4
closed
3 years ago
11
Refactor single package
#12
joeflack4
closed
3 years ago
0
NCBITaxon:9606 is missing prefix
#11
matentzn
closed
2 years ago
7
Export as RDFXML and ensure no warnings when loading with ROBOT
#10
matentzn
closed
2 years ago
4
Add makefile for building the omim.ttl file
#9
jiaola
closed
3 years ago
1
Add OWL reification for Gene-Disease association
#8
jiaola
closed
1 year ago
4
Label/synonym formatting: lowercase except for acronyms
#7
joeflack4
closed
3 years ago
9
Label & synonym capitalization updates
#6
joeflack4
closed
3 years ago
6
Do not upper-case the first letter of the label for synonyms - unless abbreviations
#5
jiaola
closed
3 years ago
0
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