Branch: refs/heads/unstable
Home: https://github.com/PathwayCommons/factoid
Commit: 00cc6978d930d9b4d28845b2b89c1f0928d6c511
https://github.com/PathwayCommons/factoid/commit/00cc6978d930d9b4d28845b2b89c1f0928d6c511
Author: Max Franz <[email protected]>
Date: 2017-12-18 (Mon, 18 Dec 2017)
Changed paths:
M package-lock.json
M package.json
M src/client/components/entity-info.js
M src/client/components/highlighter.js
M src/config.js
M src/model/element/element.js
M src/model/element/entity.js
M src/model/element/factory.js
M src/server/routes/api/document/reach.js
A src/server/routes/api/element-association/aggregate.js
A src/server/routes/api/element-association/chebi.js
M src/server/routes/api/element-association/index.js
A src/server/routes/api/element-association/pubchem.js
A src/server/routes/api/element-association/search-string-conversion.js
M src/server/routes/api/element-association/uniprot.js
M src/styles/editor/entity-info.css
M src/util/obj.js
Log Message:
-----------
Add support for association of entities with small chemical database IDS and
aggregating different types of searches.
- Support Chebi search and ID lookup.
- Support Pubchem search and ID lookup.
- Both Chebi and Pubchem webservice calls have caching.
- Remove serverside linkout URL generation. This is better handled in the UI.
- Ensure env vars that are numeric are stored as ints/floats.
- Add an aggregate search provider that handles calling multiple providers
(e.g. Uniprot and Chebi) and sorting the results intelligently.
- Revise the Uniprot provider to use an XML response. This is necessary
because Uniprot has malformed (unparseable) protein names in their
tab-delimited format. Using XML is slower.
- Allow proper formatting of chemical formulae with subscripts.
- Automatically translate "sulphur" to IUPAC-approved "sulfur" in searches to
get better results for Commonwealth scientists. More mappings can be added in
future.
- Add support for doing Pubchem queries with their table response format. This
is ~5x faster (e.g. typically 10s to 2s). This necessitates using a separate
query for synonyms. However, Pubchem can return long lists of synonyms -- many
of which aren't useful.
- Allow chemicals to be grounded from Reach. Reach uses Pubchem, but we use
Chebi (for now). So a Chebi lookup is done and cross-referenced with Chebi by
InChi.
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