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SwissProt entity completion issue #96

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wshayes opened this issue Jun 12, 2018 · 0 comments
Closed

SwissProt entity completion issue #96

wshayes opened this issue Jun 12, 2018 · 0 comments
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wshayes commented Jun 12, 2018 •
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Child of #84

Reported by Natalie: For SwissProt, I don’t seem to be able to use the label (e.g., “H4_HUMAN”) to autocomplete – no results are obtained. I see the label is listed as an alt_id in the resource file, and the associated gene symbol (in the case of H4, one of many) is used as the label. Maybe this is part of the issue?

{"term": {"namespace": "SP", "namespace_value": "P62805", "src_id": "P62805", "id": "SP:P62805", "label": "HIST1H4A", "name": "HIST1H4A", "description": "Histone H4", "species_id": "TAX:9606", "species_label": "human", "entity_types": ["Gene", "RNA", "Protein"], "synonyms": ["H4/A", "H4FA"], "equivalences": ["EG:121504", "EG:554313", "EG:8294", "EG:8359", "EG:8360", "EG:8361", "EG:8362", "EG:8363", "EG:8364", "EG:8365", "EG:8366", "EG:8367", "EG:8368", "EG:8370"], "alt_ids": ["SP:A2VCL0", "SP:P02304", "SP:P02305", "SP:Q6DRA9", "SP:Q6FGB8", "SP:Q6NWP7", "SP:H4_HUMAN"]}}

Also:
IL-6 is being converted to two tokens when completing on it in Elasticsearch. Need to review the tokenization scheme for term completion.
@wshayes wshayes self-assigned this Jun 12, 2018
@wshayes wshayes mentioned this issue Jul 2, 2018
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@ghost ghost removed the ready label Aug 24, 2018
@dependabot-preview dependabot-preview bot mentioned this issue Sep 1, 2018
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wshayes added a commit that referenced this issue Sep 4, 2018
@wshayes
Fixes #96, #101, #99 and belbio/bel_sources#96
86099d9 
Fixed issue with equivalencing - both the issue of slow equivalencing due to using up to 10 steps for equivalences and the issue that alt_ids were not included in equivalencing.

Also fixed the issue with dashes and underscores being used to tokenize text for term completion - now we only use colons and spaces for tokenization.

Also shifted api routes into a separate file.
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Bump bel from 0.10.2 to 0.11.0 belbio/bel_api
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