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biocEDAM

preliminary investigation of biocViews in relation to EDAM ontology

Installation issues

  • the curate.Rmd vignette requires that the requests, json, jsonschema and openai python modules can be imported using reticulate
  • use BiocManager::install('vjcitn/biocEDAM') to install this package

Purpose

biocViews is an ad hoc vocabulary in the form of a graphNEL instance with over 400 terms. EDAM is an OWL model of a vocabulary devoted to concepts of data analysis and data management in the biosciences. This package unites these two resources with the objective of permitting exploration that will lead to formal ontological tagging of all Bioconductor software and data packages and workflows.

Tools

bvbrowse

This function starts a shiny app that presents term-filtered sets of packages and their views annotation.

allmap

The allmap data.frame is the output of text2term applied to biocViews terms for evaluation of similarity to terms in the EDAM ontology.

> head(allmap)
                              Source Term ID    Source Term
0 http://ccb.hms.harvard.edu/t2t/RFzhTje9ucG      BiocViews
1 http://ccb.hms.harvard.edu/t2t/RFzhTje9ucG      BiocViews
2 http://ccb.hms.harvard.edu/t2t/R3hqXkeJtkt       Software
3 http://ccb.hms.harvard.edu/t2t/R4dWXrwrX3W AnnotationData
4 http://ccb.hms.harvard.edu/t2t/R4dWXrwrX3W AnnotationData
5 http://ccb.hms.harvard.edu/t2t/R4dWXrwrX3W AnnotationData
     Mapped Term Label   Mapped Term CURIE
0     GenomeReviews ID      EDAM.DATA:2751
1                 BioC    EDAM.FORMAT:3782
2 Software engineering     EDAM.TOPIC:3372
3           Annotation      EDAM.DATA:2018
4           Annotation EDAM.OPERATION:0226
5          Gene report      EDAM.DATA:0916
                         Mapped Term IRI Mapping Score Tags
0      http://edamontology.org/data_2751         0.459 None
1    http://edamontology.org/format_3782         0.380 None
2     http://edamontology.org/topic_3372         0.721 None
3      http://edamontology.org/data_2018         0.805 None
4 http://edamontology.org/operation_0226         0.805 None
5      http://edamontology.org/data_0916         0.703 None