Although resources from Hetionet have newer versions, Hetionet itself does not have an up-to-date plan for updates. To ensure AlzKB has current data, we have replicated them using the rephetio paper and source code. The following is a detailed guide for regularly replicating this process.

Gene Ontology

Download

• gene2go.gz from ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz (update daily, we downloaded on May 13, 2024)
• Entrez Gene info from ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz (update daily, we downloaded on May 13, 2024)
• go from https://purl.obolibrary.org/obo/go/go-basic.obo (V 2024-04-24)

Get GO_annotations-9606-inferred-allev.tsv from https://github.com/dhimmel/gene-ontology/blob/d57fd938f90c79152449f5cd23d3c438a19ac2f5/code/process.ipynb#L492

Extract data with code from Anatomy Gene Ontology Domains https://github.com/dhimmel/integrate/blob/master/integrate.ipynb

MeSH

Download https://nlmpubs.nlm.nih.gov/projects/mesh/MESH_FILES/xmlmesh/desc2024.xml

Get symptoms.tsv from https://github.com/dhimmel/mesh/blob/gh-pages/descriptors.ipynb

Extract data with code from Symptom Nodes https://github.com/dhimmel/integrate/blob/master/integrate.ipynb

Uberon (requires MeSH)

Download

• http://purl.obolibrary.org/obo/uberon/uberon-basic.obo (V2024-03-22)
• http://purl.obolibrary.org/obo/uberon/uberon-ext.obo (V2024-03-22)
• negative evidence df obophenotype/uberon#703 (comment)

Get human-constraint.tsv from https://github.com/dhimmel/uberon/blob/gh-pages/human-constraint.ipynb

Get hetio-slim.tsv from https://github.com/dhimmel/uberon/blob/gh-pages/process.ipynb

Extract data with code from Anotomy Nodes https://github.com/dhimmel/integrate/blob/master/integrate.ipynb

DrugCentral (requires Disease Ontology)

DrugBank

• Download drugbank.xml.gz from https://go.drugbank.com/releases/latest (V5.1.12 2024-03-14)
• Get drugbank-slim.tsv from https://github.com/dhimmel/drugbank/blob/gh-pages/parse.ipynb

DrugCentral

• Download DrugCentral database dump file from https://drugcentral.org/download (V 2023-11-01)
• Install PostgreSQL from https://www.enterprisedb.com/downloads/postgres-postgresql-downloads based on https://www.postgresql.org/download/macosx/
• Import table dump (.SQL) using pgAdmin based on https://stackoverflow.com/questions/18736345/export-and-import-table-dump-sql-using-pgadmin
• Get pharm_class.tsv & identifiers.tsv from the database above by running the following query and save as tsv
  • SELECT * FROM public.pharma_class
  • SELECT * FROM public.identifier (previously: https://github.com/olegursu/drugtarget/tree/9a6d84bed8650c6c507a2d3d786814c774568610)

Get classes.tsv & drug-to-class.tsv from https://github.com/dhimmel/drugcentral/blob/master/drugcentral-to-rephetio.ipynb

Extract data with code from Pharmacologic Classes (Add 'Chemical Structure' to class_types) https://github.com/dhimmel/integrate/blob/master/integrate.ipynb

MEDLINE (requires MeSH & DiseaseOntology)

Download a slim DO https://think-lab.github.io/d/44/#144

Download HumanDO.obo https://github.com/DiseaseOntology/HumanDiseaseOntology/blob/main/src/ontology/HumanDO.obo (V 2024-03-28)

Reads DO Slim terms and generates slim-specific datasets https://github.com/dhimmel/disease-ontology/blob/gh-pages/slim.ipynb

Get disease-disease-cooccurrence.tsv from https://github.com/hetio/medline/blob/main/diseases.ipynb

Get disease-symptom-cooccurrence.tsv from https://github.com/hetio/medline/blob/main/symptoms.ipynb

Get disease-uberon-cooccurrence.tsv from https://github.com/hetio/medline/blob/main/tissues.ipynb

Extract data with code from Symptom edges https://github.com/dhimmel/integrate/blob/master/integrate.ipynb

BindingDB

UniProt

• Download idmapping.dat.gz from https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz (readme: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/README ) (V 2024-05-13)
• Get GeneID.tsv.gz from https://github.com/dhimmel/uniprot/blob/gh-pages/mappings.ipynb

Entrez-Gene

• Use Homo_sapiens.gene_info.gz as same as NCBI data resource (The data update daily, we downloaded on May 13, 2024)
• Get genes-human.tsv from https://github.com/dhimmel/entrez-gene/blob/gh-pages/process.ipynb

Drugbank

• Get drugbank.tsv, drugbank-slim.tsv, and proteins.tsv from https://github.com/dhimmel/drugbank/blob/gh-pages/parse.ipynb

Drugcentral

• Download Drug-target interaction data from https://drugcentral.org/download (previously: https://github.com/olegursu/drugtarget/blob/9a6d84bed8650c6c507a2d3d786814c774568610/drug_target.tsv )
• Get targets.tsv from https://github.com/dhimmel/drugcentral/blob/master/drugcentral-to-rephetio.ipynb

BindingDB

• Get bindingdb.tsv from https://github.com/dhimmel/drugbank/blob/6b9ae386d6ba4a0eca2d66d4b0337a6e90fe81f4/unichem-map.ipynb
• Download BindingDB_All_202405_tsv.zip from https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp
• Get binding.tsv.gz from https://github.com/dhimmel/bindingdb/blob/gh-pages/process.ipynb
• Get bindings-drugbank-gene.tsv from https://github.com/dhimmel/bindingdb/blob/gh-pages/collapse.Rmd

Compile

• Get CbG-binding.tsv from https://github.com/dhimmel/integrate/blob/master/compile/CbG-binding.ipynb

Extract data with code from Compound bindings https://github.com/dhimmel/integrate/blob/master/integrate.ipynb