marcin p. joachimiak
marcin p. joachimiak
We are interested in global analysis of the FooDB data to identify similar food subgroups and to find potential therapies to remedy excess/deficit of chemical compounds in specific human conditions....
Using this notebook as an example: https://nbviewer.org/github/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb I am having trouble with this import: w = GraphRenderer.create('png') which gives error: ModuleNotFoundError: No module named ‘ontobio.graph_io’ Context: I did pip install...
When trying to obtain the GO subgraph for 800 input terms, as here: https://github.com/kbaseIncubator/KE_KG/blob/main/src/embeddings/GO_ontobio.ipynb I am running into the recursion limit RecursionError: maximum recursion depth exceeded. I can set the...
The new Monarch beta API is not serving inferred phenotypes and added some EFO terms. The corresponding Monarch ticket is: https://github.com/monarch-initiative/dipper/issues/824 From Kent: "for HPO terms, there is some discussion...
I have been using this call to retrieve disease-phenotype associations from Monarch: with urllib.request.urlopen("https://api.monarchinitiative.org/api/mart/disease/phenotype/NCBITaxon%3A9606") as url: disease_phenotype_data.append(json.loads(url.read().decode())) It appears that there is no way to retrieve based on specified relationships...
**Is your feature request related to a problem? Please describe.** Based on KG-Microbe builds there are terms from OBO ontologies (eg ChEBI and GO) which get dropped from the transform...
**Name of the dataset** COVID-19 Disease Map https://pubchem.ncbi.nlm.nih.gov/#query=COVID-19%20Disease%20Map&tab=pathway&source=COVID-19%20Disease%20Map **Mapping or relevant fields** A clear and concise description of what which fields you would want to be ingested. If possible, highlight...
### Describe the desired behavior Especially in the dashboard sankey plot, we may want to do log of counts for categories since everything is dominated by Protein and OntologyClass. ##...