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  1. NIF
  2. NIF-11672

Integrate Orphanet into DO

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    • NIF
    • Issues closed as MONARCH has transitioned from UCSD services

    Description

      We need orphanet disease ids properly added and xrefed/equivanced with the DOID.

      There are a couple of relevant files:

      The Orphanet rare disease ontology:
      http://www.orphadata.org/cgi-bin/inc/ordo_orphanet.inc.php

      Diseases cross-referenced with other nomenclatures:
      http://www.orphadata.org/cgi-bin/inc/product1.inc.php

      Diseases and their clinical signs:
      http://www.orphadata.org/cgi-bin/inc/product4.inc.php
      (these might be able to be used to map to HPO or other vocabs for the atomic phenotypes...not sure if this is appropriate to do in this ticket)

      The disease xref xml has been imported into NIF/DISCO, but not yet exposed. If you prefer to use a flattened version of the file, let me know and I will write a view to expose it (nif-0000-21306). It houses mappings to OMIM, ICD10, MESH, UMLS, MEDDRA, SNOMED CT.

      also see https://github.com/monarch-initiative/disease-miner/issues/7

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          breaks down

          Task - A task that needs to be done. NIF-11856 Improvements to DO for 1.0 release

          • Critical - Crashes, loss of data, severe memory leak.
          • Closed
          is related to

          New Feature Request - A new feature of the product, which has yet to be developed. NIF-11632 Import Orphanet rare disease summary information

          • Major - Major loss of function.
          • Closed

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              sessaid Shahim Essaid
              nlw Nicole Washington
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