ontobio
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biolink
python library for working with ontologies and ontology associations
The Makefile has a target to run travis tests. These respresent only some tests (called "local" in a comment). Travis should run all, or as many tests as is reasonable,...
Make sure that ontobio gaf parsing covers the with/from column and anywhere else we encounter GO term IDs.
GAF is a denormalized format so there is necessarily repetition of information Any such repetition should be consistent. E.g. info about a gene product is repeated (symbol, description, synonyms). Any...
Sorry if there's already functionality like this in ontobio: Use case is generating a new Panther slim from an Ontology object. We first load the whole GO, run some heuristic...
While parsing GAFs etc ontobio will construct expressions for each line and send them to an inference engine to determine if the annotations are (a) taxonomically invalid or otherwise logically...
This came from work on the AGR loader. We needed to clean up the xref URLs (node["meta"]["definition"]["xrefs"]) extracted from the DO file and were thinking this could just be incorporated...
E.g. remove all cell component; remove all with a particular subset (antislim) request from: @putmantime for Translator QC notebook
To keep the runtime down and efficient, can make assumption that gene products are always continguous. redundancy only needs tested on a per gp basis. behavior could be configurable, but...
http://nbviewer.jupyter.org/github/biolink/ontobio/blob/master/notebooks/PTSD_Genes.ipynb this notebook shows the following error: ``` --------------------------------------------------------------------------- NameError Traceback (most recent call last) in () ----> 1 proteins = wd.canned_query('genetic_association', doid) NameError: name 'doid' is not defined ```
