Justin Reese

Improve normalization of proteins

1

### Describe the bug At least some proteins need normalization - e.g. ACE2: ``` UniProtKB:Q9BYF1 ACE2 pharmgkb|intact|go-cams NCBIGene:59272 ACE2 zhou_host_proteins|SciBite-CORD-19 ENSEMBL:ENSG00000130234 ACE2 STRING # this is the gene, so a...

Create system for checking graph schema, starting with TTD (one of our simpler ingest)

2

Per convo with Nico, it would be good to have a system for checking/validating the schema of our graph. A good start would be to make RDF for one simple...

### Describe the bug The index.html is malformed in the build base directories, for example: https://kg-hub.berkeleybop.io/kg-covid-19/20201001/index.html ``` Files No files in this directory. ats/index.html">stats transformed ``` ### To Reproduce Go...

Consider moving curated GPI file to our data repo

1

Right now the curated GPI file for SARS-CoV-2 proteins and cleavage products lives here: https://github.com/Knowledge-Graph-Hub/kg-covid-19/tree/master/curated/ORFs We should consider moving this here to this repo for data we ingest: https://github.com/Knowledge-Graph-Hub/kg-covid-19-data This...

### Describe the desired behavior Right now in Jenkins we manually add a (blank) directory for each existing build in our projectdir: https://github.com/Knowledge-Graph-Hub/kg-covid-19/blob/4a1fda723602b90f2ef22da43452f15a82e883ed/Jenkinsfile#L175 on the command-line. A better solution would...

This could be part of the QC process, possibly with some granularity with respect to what is done when the SPARQL query fails - some failures might not failing the...

Develop a way to deal with time series data

1

Per convo with @realmacin @cmungall @justaddcoffee @wdduncan We'd like a simple way of modeling time series data, for example these use cases: - clinical course of patients over time (time...

**Name of the dataset** Ingest drug -> target information from SMS, available here are a tar file: https://labsyspharm.shinyapps.io/smallmoleculesuite/_w_4fb0f5cc/sms/assets/downloads/sms_tables_chembl_v25.tar **Mapping or relevant fields** A good start would be to map drugs...

Ingests that use symmetric edge_labels (like interacts_with) should assert edge in both directions

1

### Describe the bug Some ingests like IntAct and STRING use symmetric edge labels like `interacts_with`. These should assert in both directions: if ingest asserts: `A interacts_with B` it should...

**Name of the dataset** Peter's software here ingests clinical trial data from clinicaltrials.gov https://github.com/monarch-initiative/yactp and outputs a CSV that should be easily parsable. **Mapping or relevant fields** If possible, highlight...