Mapping of CAIRR BioProject fields to NCBI BioProject XML

[martinjoconnor]

Determine mappings from CAIRR BioProject fields to NCBI BioProject XML.

The following are the BioProject fields in the CAIRR template:

These need to be mapped to NCBI BioProject XML, e.g.,

<Project>

  <ProjectID/>                          

  <Descriptor>

    <Title>Candida albicans A123</Title>
    <Description> <p> Genome Sequencing of C. albicans </p> </Description>
    <ExternalLink category="Related Resources" label="Genomics Institute">
      <URL>www.organization.org</URL>
    </ExternalLink>

    <Relevance> <Medical>yes</Medical> </Relevance>

  </Descriptor>

  <ProjectType>
    <!-- sample-scope = eMonoisolate eMultiisolate eMultispecies eEnvironment eSynthetic eSingleCell eOther -->

    <ProjectTypeSubmission sample_scope="eMonoisolate">

      <Organism>
        <OrganismName>Candida albicans A123</OrganismName>
        <Strain>A123</Strain>
      </Organism>

      <BioSampleSet>
        <BioSample>
          <PrimaryId db="BioSample">SAMN000123</PrimaryId>
        </BioSample>
      </BioSampleSet>

      <IntendedDataTypeSet>
        <DataType>
          genome sequencing
          <!--
              genome sequencing raw sequence reads genome sequencing and assembly
              metagenome metagenomic assembly assembly transcriptome proteomic map
              clone ends targeted loci targeted loci cultured targeted loci
              environmental random survey exome variation epigenomics phenotype or genotype other
          -->
        </DataType>
      </IntendedDataTypeSet>

    </ProjectTypeSubmission>
  </ProjectType>

</Project>

Some fields already go to the Description element in a submission:

    <Description>
        <Comment>AIRR (myasthenia gravis) data to the NCBI using the CAIRR</Comment>
        <Submitter user_name="ahmadchan@gmail.com"/>
        <Organization type="lab" role="owner">
            <Name>Yale University</Name>
            <Contact email="ahmad.chan@yale.edu">
                <Name>
                    <First>Kevin</First>
                    <Last>O'Connor</Last>
                </Name>
            </Contact>
        </Organization>
    </Description>

[martinjoconnor]

Email from Ahmad:

We already have defined a mapping from MiAIRR BioProject to NCBI BioProject https://github.com/airr-community/airr-standards/blob/master/NCBI_implementation/mapping_MiAIRR_BioProject.tsv. 
Here "key relation" column tells whether we have an exact matching of MiAIRR elements to NCBI elements or not (we represent those fields as MiAIRR custom fields). 
Please let me know if you need more information.