ontobio
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biolink
python library for working with ontologies and ontology associations
When I run this code in my own notebook, http://nbviewer.jupyter.org/github/biolink/ontobio/blob/master/notebooks/Mouse_Gene_Phenotypes.ipynb ``` z, xlabels, ylabels = aset.similarity_matrix(diseases, diseases) import plotly.plotly as py import plotly.graph_objs as go import numpy as np trace...
http://nbviewer.jupyter.org/github/biolink/ontobio/blob/master/notebooks/GO_Functional_Similarity.ipynb starting from cell 10 there are multiple stack traces such as ``` ERROR:pysolr:Connection to server 'http://golr.berkeleybop.org/select/?q=%2A%3A%2A&fq=document_category%3A%22annotation%22&fq=taxon_closure%3A%22NCBITaxon%3A7955%22&facet=off&facet.limit=0&facet.mincount=1&fl=bioentity%2Cbioentity_label%2Cqualifier%2Cannotation_class&rows=100000&wt=json' timed out: HTTPConnectionPool(host='golr.berkeleybop.org', port=80): Read timed out. (read timeout=4) Traceback (most recent call...
We should make it easier to setup a virtual env. Right now the developer has to go to rtd, and the instructions there are out of date (pyvenv rather than...
We will move the json-ld context file from prefixcommons repo to biolink once this percolates to a new version of curie_util on pypi https://github.com/prefixcommons/prefixcommons-py/pull/9 we will make a new ontobio...
``` WB WBGene00011392 involved_in GO:0010466 PMID:9726255|WB_REF:WBPaper00003188 IDA 20090318 WB ``` Is an example of a gpad line from wb.gpad. IDA should be an ECO id.
Currently the GAF to RDF transformation does not include taxon information for the gene product. This information will be desired when the RDF is more utilized. Let's add this to...
_From @murphyte on July 6, 2018 20:23_ Hi GO -- Some data files have recently shown a change where column 13 has the string "NCBITaxon:" with no value for some...
As it stands now, there is no way of knowing what calls are coming from biolink/ontobio except by knowing IP addresses. It should be standard to have all HTTP calls...
Currently there are hardly any tests for RDF generation from GAF lines. The logic is complicated enough that we should work to produce a relatively sophisticated system that really defines...