Peter Robinson

Improve Exomiser HTML

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In recent work, we are getting on the order of 50-100 HPO terms per proband (from EHR text mining). This makes the current output of Exomiser unweildly. Even with smaller...

In about 1% of cases, Exomiser shows incorrect phenotype matches for pairs of terms that pertain to different organ systems. e.g. HP:0000486, Strabismus - MP:0001513, limb grasping (Eye and musculoskeletal...

Compilation error in PhenotypeMatchServiceTest

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Error:(92, 9) java: method does not override or implement a method from a supertype this is the offending code ``` @Override public String getLabel() { return ""; } ``` and...

Text mining bug

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Scigraph returns two terms for this text Myopathic facies 1. Myopathic facies 2. Myopathy This does not make sense because if we find a good match for a longer phrase,...

deadlinks

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It is unclear how to use the links underneath this part of the README: Check out some of the REST endpoints (they point to services on localhost which doesnot make...

og2dot missing from Find_All_Paths

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The following code from http://nbviewer.jupyter.org/github/biolink/ontobio/blob/master/notebooks/Find_All_Paths.ipynb ``` from ontobio.io.ontol_renderers import GraphRenderer w = GraphRenderer.create('png') w.outfile = 'output/multipath.png' w.write(subont,query_ids=sample_path) ``` fails with the error message ``FileNotFoundError: [Errno 2] No such file or...

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 ```

Mouse_Gene_Phenotypes error

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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...

Null pointer with Node.getType()

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I am using phenol (https://github.com/monarch-initiative/phenol) to parse the example GO obo file in that repository. It seems to be picking up this as a Node: ``` synonymtypedef: syngo_official_label "label approved...