Configure

1. Make a directory for your ingest, using the source of the data as the name:

   mkdir src/monarch_ingest/ingests/<source> 
   

   For example:

   mkdir src/monarch_ingest/ingests/ncbi
   

2. Add data sources to src/monarch_ingest/download.yaml:

   # <source>
   -
     url: https://<source>.com/downloads/somedata.txt 
     local_name: data/<source>/somedata.txt
     tag: <source>_<ingest>                             
   

   For example:

   # mgi
   -
     url: http://www.informatics.jax.org/downloads/reports/MRK_Reference.rpt
     local_name: data/mgi/MRK_Reference.rpt
     tag: mgi_publication_to_gene   
   

   Note: You can now use ingest download --tags <tag> or ingest download --all, and your data will be downloaded to the appropriate subdir in data/

3. Add your ingest to src/monarch_ingest/ingests.yaml:

   <ingest_name>:
     config: 'ingests/<source>/<ingest>.yaml
   

   For example:

   ncbi_gene:
     config: 'ingests/ncbi/gene.yaml'
   

4. Copy the template:

   cp ingest_template/* src/monarch_ingest/ingests/<source>
   

5. Edit metadata.yaml:

   • Update the description, rights link, url, etc and then add your source_file

6. Edit the source file yaml

   • Match the columns or required fields with what's available in the file to be ingested
     • If it's an ingest that exists in Dipper, check out what Dipper does.
     • Check the Biolink Model documentation to look at what you can capture
     • If what we need from an ingest can't be captured in the model yet, make a new Biolink issue
   • Set the header properties
     • If there is no header at all, set header: False
     • If there are comment lines before the header, count them and set skip_lines: {n}

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