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submission prep script
abradyIGS edited this page Feb 10, 2022
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python prepare_C2M2_submission.py (previously build_term_tables.py) is a Python script that builds C2M2 controlled-vocabulary (CV) term usage tables for anatomy, assay type, file data type, file format, disease and taxonomy metadata.
0. First build your file.tsv, biosample.tsv, biosample_disease.tsv, subject_disease.tsv, and subject_role_taxonomy.tsv tables. (Some of these can be left empty (as header-only TSVs) if desired: see the C2M2 table wiki for requirements.)
2. Download the CV reference files [Last updated 9/7/21] at OSF (select external_CV_reference_files and then 'Download as zip'.)
5. Edit line 42 of the script to match the location of your file.tsv, biosample.tsv, (etc.) TSV files
This script is under active development: please contact us with any questions by emailing the helpdesk at [email protected] or posting to Discussions
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Tutorials
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C2M2 Table Guide
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Table Summary
- analysis_type.tsv
- anatomy.tsv
- assay_type.tsv
- biofluid.tsv
- biosample.tsv
- biosample_disease.tsv
- biosample_from_subject.tsv
- biosample_gene.tsv
- biosample_in_collection.tsv
- biosample_ptm.tsv
- biosample_substance.tsv
- collection.tsv
- collection_anatomy.tsv
- collection_biofluid.tsv
- collection_compound.tsv
- collection_defined_by_project.tsv
- collection_disease.tsv
- collection_gene.tsv
- collection_in_collection.tsv
- collection_phenotype.tsv
- collection_protein.tsv
- collection_ptm.tsv
- collection_substance.tsv
- collection_taxonomy.tsv
- compound.tsv
- data_type.tsv
- dcc.tsv (formerly
primary_dcc_contact.tsv - disease.tsv
- domain_location.tsv
- file.tsv
- file_describes_biosample.tsv
- file_describes_collection.tsv
- file_describes_subject.tsv
- file_format.tsv
- file_in_collection.tsv
- gene.tsv
- id_namespace.tsv
- ncbi_taxonomy.tsv
- phenotype.tsv
- phenotype_disease.tsv
- phenotype_gene.tsv
- project.tsv
- project_in_project.tsv
- protein.tsv
- protein_gene.tsv
- ptm.tsv
- ptm_type.tsv
- ptm_subtype.tsv
- sample_prep_method.tsv
- subject.tsv
- subject_disease.tsv
- subject_in_collection.tsv
- subject_phenotype.tsv
- subject_race.tsv
- subject_role_taxonomy.tsv
- subject_substance.tsv
- substance.tsv
- Reference Tables
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Table Summary