Details
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Task
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Resolution: Canceled
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Critical
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None
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MONARCH 1.0
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None
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NIF
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Issues closed as MONARCH has transitioned from UCSD services
Description
For our first major release, we need some major improvements to our uberdisease ontology (to be merged back with the standard DO).
Examples:
*integration of Orphanet
*integration with MEDIC and UMLS mappings
*integration with MESH
*integration with Clinvar and MedGen mappings
*add all OMIM ids/labels
This may require some hand-curation; others may require updates to the DO itself; and updates to the automated pipeline.
Attach specific tickets to this task.
Relevant repositories:
https://github.com/obophenotype/human-disease-ontology (this is the current repository, where new files sit)
https://github.com/monarch-initiative/disease-miner (the experimental monarch version of DO)
http://sourceforge.net/p/diseaseontology/feature-requests/ (the old one, i think it's now migrated to git)
http://disease-ontology.org/
https://code.google.com/p/phenotype-ontologies/issues/list (some issues are here, but should be migrated)
https://build.berkeleybop.org/job/build-doid/ (the jenkins job for the first in this list, the doid)
Here's some documentation for disease-miner, about the experimental pipeline:
https://docs.google.com/document/d/1y08_R1P98lm2rRu6VMRWLK5bvSAe-FzU86jD_qaXGSE/edit#
Attachments
Issue Links
- is blocked by
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NIF-11620 many OMIM classes missing
- Closed
- is broken down by
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NIF-11621 purl for omim ids doesn't resolve
- Closed
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NIF-11644 need to standardize ontology prefixes in DO
- Closed
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NIF-11720 Make monarch.owl pull newest DO file
- Closed
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NIF-11639 Add external disease vocabularies to DO, even without hierarchy
- Closed
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NIF-11663 run diseaseminer updates on jenkins
- Closed
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NIF-11664 Add clinvar disease/traits to DO
- Closed
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NIF-11672 Integrate Orphanet into DO
- Closed
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NIF-11686 add KEGG disease id mappings
- Closed
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NIF-11766 add medgen ids to uberdisease
- Closed
- is related to
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NIF-11604 fix SNOMED prefixes in DO
- Closed
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NIF-11609 many merging classes are missing from DO
- Closed