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Specifically among 79 name-identical pathway groups 52 remained incompletely unified, again suggesting a limited usefulness for unifying based on pathway names.
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We recently developed an integrated pathway database, PathwayAPI [ 3], which utilises a novel pathway merging approach based on pathway name matches (Longest Common Substring matching; LCS) [ 3].
For the more conventional use, CANGES enables focal gene search based on the pathway name and SNP retrieval for a custom gene list.
Custom Python scripts (available on request) were used to extract the protein groups and corresponding protein sequences for each locus in the RdDM pathway based on the gene names used for A r. thaliana (reference proteins, supplementary table S1, Supplementary Material online).
The Event Ontology covers (i) classification of molecular interactions, (ii) relations between pathways and subpathways, (iii) relations between pathways and biological phenomena, (iv) classification of subpathways based on molecule names (MoleculeRole Ontology) and (v) relations between subpathways and regulated pathways.
Users can query the database based on allergen name, organism name, pathway or bibliographical references.
The Web-based search engine is able to search for locations based on area names, building names, and groups of landmark types, business names, and business categories.
Responses were analyzed based on group names and codes.
Name conversions to Ensemble gene names are done based on alternative names provided from Ensembl 48.
Matches were primarily based on company names.
Below diagonal: F ST based on variety names (see Methods).
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