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TableInfo: file.tsv
abradyIGS edited this page Sep 3, 2021
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The file.tsv table will contain one row for each file in your program.
| Field | Field Description | Required? | Field Value Type | Extra Info |
|---|---|---|---|---|
| id_namespace | A CFDE-cleared identifier representing the top-level data space containing this file [part 1 of 2-component composite primary key] | Required | string |
id_namespace is a unique URI prefix pre-registered with CFDE and attached to your program (or a subset of your program) that identifies anything labeled with it as belonging to you. Please see the technical documentation for a full discussion of how this information is built and used. |
| local_id | An identifier representing this file, unique within this id_namespace [part 2 of 2-component composite primary key] | Required | string | The string formed by concatenating the id_namespace and local_id field values must be unique for each row in this table. Please see the technical documentation for a full discussion of how this information is to be used. |
| project_id_namespace | The id_namespace of the primary project within which this file was created [part 1 of 2-component composite foreign key] | Required | string | |
| project_local_id | The local_id of the primary project within which this file was created [part 2 of 2-component composite foreign key] | Required | string | |
| persistent_id | A persistent, resolvable (not necessarily retrievable) URI or compact ID permanently attached to this file | Optional | string | Meant to serve as a permanent address to which landing pages (which summarize metadata associated with this file) and other relevant annotations and functions can optionally be attached, including information enabling resolution to a network location through which the file can be accessed. Actual network locations must not be embedded directly within this identifier: one level of indirection is required in order to protect persistent_id values from changes in network location over time as files are moved around. Please see the technical documentation for a full discussion of how this information is to be used. |
| creation_time | An ISO 8601 -; RFC 3339 (subset)-compliant timestamp documenting this file's creation time: YYYY-MM-DDTHH:MM:SS±NN:NN | Non-required: Any number of rows after the header can be filled | Value must be datetime | Example valid dates:2021-01-082021-01-08T00:45:40Z2021-01-08T00:45:40+00:00
|
| size_in_bytes | The size of this file in bytes | Non-required: Any number of rows after the header can be filled | Value type is integer | do not include decimal places or decimal sign (.) |
| uncompressed_size_in_bytes | The total decompressed size in bytes of the contents of this file | Non-required: Any number of rows after the header can be filled | Value type is integer | do not include decimal places or decimal sign (.) |
| sha256 | (preferred) SHA-256 checksum for this file [sha256, md5 cannot both be null] | Either this field OR md5 must be populated | Value should be HSA-256 hash or nothing; If you have both please use sha256 | You may populate both md5 and sha256 for a given row, but only one is required |
| md5 | (allowed) MD5 checksum for this file [sha256, md5 cannot both be null] | Either this field OR sha256 must be populated | Value should be MD5 hash or nothing; If you have both, please use sha256. | You may populate both md5 and sha256 for a given row but only one is required |
| filename | A filename with no prepended PATH information. | Non-required: Any number of rows after the header can be filled | Value type is string | Filenames do not need to be unique. Uniqueness is ensured by the local_id |
| file_format | An EDAM CV term ID identifying the digital format of this file (e.g. TSV or FASTQ) | Non-required: Any number of rows after the header can be filled | Value must be a valid EDAM ID |
EDAM format lookup Example valid EDAM IDs: format:1930format:3712format:2310
|
| data_type | An EDAM CV term ID identifying the type of information stored in this file (e.g. RNA sequence reads) | Non-required: Any number of rows after the header can be filled | Value must be a valid EDAM ID |
EDAM data type lookup Example valid EDAM IDs: data:2044data:2050data:2082
|
| assay_type | An OBI CV term ID describing the type of experiment that generated the results summarized by this file | Non-required: Any number of rows after the header can be filled | Value must be a valid OBI ID |
OBI lookup service Example valid OBI IDs: OBI:0000366OBI:0001177OBI:0002763
|
| mime_type | A MIME type describing this file | Non-required: Any number of rows after the header can be filled | Value must be a valid MIME type |
Common MIME types Tutorial for bulk MIME type identification Example valid MIME types: image/jpegtext/htmlapplication/octet-stream
|
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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_protein.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