Comments (4)
From: Ebrahim Bagheri [...]
To: obo-discuss [email protected]
Subject: [obo-discuss] UMLS to DBpedia Mappings
Date: Thu, 19 Apr 2018 05:28:59 -0700 (PDT)We are pleased to announce our work on mapping between UMLS and DBpedia
concepts has been published in the “Journal of the American Medical
Informatics Association” (https://doi.org/10.1093/jamia/ocy021) with the
full dataset, online browser, and RESTful API available at
http://denote.rnet.ryerson.ca/umlsMap/. This dataset includes 221 690
“exact match” relations, 26 276 “close match”, and 6 784 322 “see also”
pairings. We hope you find this useful in facilitating effective
interchange and integration between general knowledge databases (DBpedia)
and those from (bio)medical ontologies (UMLS).
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@stuppie has done the bulk of the work here: https://github.com/stuppie/semmed-biolink
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@stuppie @andrewsu how are we doing on this?
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We have the first iteration of a Biolink-compliant version of semmeddb here http://34.229.55.225:7474/browser/
It is biolink-compliant as of a week ago.
But.. I'm not sure what a "converter" is ?
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Related Issues (20)
- migrate KGX to poetry HOT 1
- remove knowledge source parameters from node files (instead rely on provided_by for nodes) HOT 4
- TSV->TSV transform ignores transform-level metadata about knowledge sources
- Add ability to "turn off" KGX's prefix mapping functionality
- KGX edge merge does not take into account enough attributes on the edge HOT 1
- add documentation to the kgx merge doc that shows when to use cat-merge as well as a set of steps to use merge config
- Dynamic configuration of Biolink Model semantics in KGX validation
- Knowledge Graph Exchange (KGE) Archive Download
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- Do the KGX serialization formats support representation of Biolink qualifiers? HOT 2
- Error occurs when specifying a version starting with "v" in get_biolink_model_schema method HOT 1
- remove pinning of docutils==0.16.0 so that downstream users can also use sphinx
- Option to add un-prefixed labels in neo4j labels
- Automate mapping of infores in primary_knowledge_source HOT 1
- Fetching biolink-model for validate is confused by `v` in biolink version HOT 1
- run kgx validate from inside the project - need scripts defined in pyproject.toml HOT 2
- kgx validate `-o` option writes an empty file, output goes to stderr rather than stdout
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- add SQL sink
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