cfde_schema
A complete list of schematic specifications for the resources (TSV table files) that will be used to represent C2M2 DCC metadata prior to ingest into the C2M2 database system
URI: https://w3id.org/linkml/cfde Name: cfde_schema
Classes
| Class | Description |
|---|---|
| AnalysisType | List of Ontology for Biomedical Investigations (OBI) CV terms used to describe analytic methods that generate C2M2 files |
| Anatomy | List of Uber-anatomy ontology (UBERON) CV terms used to locate the origin of a C2M2 biosample within the physiology of its source or host organism |
| AssayType | List of Ontology for Biomedical Investigations (OBI) CV terms used to describe types of experiment that generate C2M2 biosamples or results stored in C2M2 files |
| Biosample | A tissue sample or other physical specimen |
| BiosampleDisease | Association between a C2M2 biosample and a disease positively (e.g. cancer tumor tissue sample) OR negatively (e.g. cancer-free tissue sample) identified for that biosample |
| BiosampleFromSubject | Association between a biosample and its source subject |
| BiosampleGene | Association between a C2M2 biosample and an Ensembl gene especially relevant to it |
| BiosampleInCollection | Association between a biosample and a (containing) collection |
| BiosampleSubstance | Association between a C2M2 biosample and a PubChem substance experimentally associated with that biosample |
| Collection | A grouping of C2M2 files, biosamples and/or subjects |
| CollectionAnatomy | Association between an UBERON anatomical term and a C2M2 collection containing experimental resources directly related to the study of the anatomical concept described by that term |
| CollectionCompound | Association between a compound and a C2M2 collection containing experimental resources directly related to the study of that compound |
| CollectionDefinedByProject | (Shallow) association between a collection and a project that defined it |
| CollectionDisease | Association between a disease and a C2M2 collection containing experimental resources directly related to the study of that disease |
| CollectionGene | Association between a gene and a C2M2 collection containing experimental resources directly related to the study of that gene |
| CollectionInCollection | Association between a containing collection (superset) and a contained collection (subset) |
| CollectionPhenotype | Association between a phenotype and a C2M2 collection containing experimental resources directly related to the study of that phenotype |
| CollectionProtein | Association between a protein and a C2M2 collection containing experimental resources directly related to the study of that protein |
| CollectionSubstance | Association between a substance and a C2M2 collection containing experimental resources directly related to the study of that substance |
| CollectionTaxonomy | Association between a taxon and a C2M2 collection containing experimental resources directly related to the study of that taxon |
| Compound | List of (i) GlyTouCan terms or (ii) PubChem 'compound' terms (normalized chemical structures) referenced in this submission; (ii) will include all PubChem 'compound' terms associated with any PubChem 'substance' terms (specific formulations of chemical materials) directly referenced in this submission, in addition to any 'compound' terms directly referenced |
| DataType | List of EDAM CV 'data:' terms used to describe data in C2M2 files |
| Dcc | The Common Fund program or data coordinating center (DCC, identified by the given project foreign key) that produced this C2M2 instance |
| Disease | List of Disease Ontology terms used to describe diseases recorded in association with C2M2 subjects or biosamples |
| File | A stable digital asset |
| FileDescribesBiosample | Association between a biosample and a file containing information about that biosample |
| FileDescribesCollection | Association between a summary file and an entire collection described by that file |
| FileDescribesSubject | Association between a subject and a file containing information about that subject |
| FileFormat | List of EDAM CV 'format:' terms used to describe formats of C2M2 files |
| FileInCollection | Association between a file and a (containing) collection |
| Gene | List of Ensembl genes directly referenced in this C2M2 submission |
| IdNamespace | A table listing identifier namespaces registered by the DCC submitting this C2M2 instance |
| NcbiTaxonomy | List of NCBI Taxonomy Database IDs identifying taxa used to describe C2M2 subjects |
| Phenotype | List of Human Phenotype Ontology terms used to describe phenotypes recorded in association with C2M2 subjects |
| PhenotypeDisease | Association between a Human Phenotype Ontology term and a Disease Ontology term identifying a disease especially relevant to it |
| PhenotypeGene | Association between a Human Phenotype Ontology term and an Ensembl gene especially relevant to it |
| Project | A node in the C2M2 project hierarchy subdividing all resources described by this DCC's C2M2 metadata |
| ProjectInProject | Association between a child project and its parent |
| Protein | List of UniProtKB proteins directly referenced in this C2M2 submission |
| ProteinGene | Association between a UniProtKB protein term and an Ensembl term identifying a gene encoding that protein |
| Subject | A biological entity from which a C2M2 biosample can in principle be generated |
| SubjectDisease | Association between a C2M2 subject and a disease positively OR negatively clinically identified in that subject |
| SubjectInCollection | Association between a subject and a (containing) collection |
| SubjectPhenotype | Association between a C2M2 subject and a phenotype positively OR negatively clinically identified for that subject |
| SubjectRace | Identification of a C2M2 subject with one or more self-selected races |
| SubjectRoleTaxonomy | Trinary association linking IDs representing (1) a subject, (2) a subject_role (a named organism-level constituent component of a subject, like 'host', 'pathogen', 'endosymbiont', 'taxon detected inside a microbiome subject', etc.) and (3) a taxonomic label (which is hereby assigned to this particular subject_role within this particular subject) |
| SubjectSubstance | Association between a C2M2 subject and a PubChem substance experimentally associated with that subject |
| Substance | List of PubChem 'substance' terms (specific formulations of chemical materials) directly referenced in this C2M2 submission |
Slots
| Slot | Description |
|---|---|
| abbreviation | A very short display label for this project |
| age_at_enrollment | The age in years (with a fixed precision of two digits past the decimal point) of this subject when they were first enrolled in the primary project within which they were studied |
| age_at_sampling | The age in years (with a fixed precision of two digits past the decimal point) of this subject when this biosample was taken |
| analysis_type | An OBI CV term ID describing the type of analytic operation that generated this file |
| anatomy | An UBERON CV term ID used to locate the origin of this biosample within the physiology of its source or host organism |
| assay_type | An OBI CV term ID describing the type of experiment that generated the results summarized by this file |
| association_type | The relationship between this biosample and this disease (e.g. 'observed' or '(tested for, but) not observed') |
| biosample_id_namespace | Identifier namespace for this biosample |
| biosample_local_id | The ID of this biosample |
| bundle_collection_id_namespace | If this file is a bundle encoding more than one sub-file, this field gives the id_namespace of a collection listing the bundle's sub-file contents; null otherwise |
| bundle_collection_local_id | If this file is a bundle encoding more than one sub-file, this field gives the local_id of a collection listing the bundle's sub-file contents; null otherwise |
| child_project_id_namespace | ID of the identifier namespace for the child in this parent-child project pair |
| child_project_local_id | The ID of the contained (child) project |
| clade | The phylogenetic level (e.g. species, genus) assigned to this taxon |
| collection_id_namespace | Identifier namespace for this collection |
| collection_local_id | The ID of this collection |
| compound | A PubChem or GlyTouCan term ID describing this compound |
| compression_format | An EDAM CV term ID identifying the compression format of this file (e.g. gzip or bzip2): null if this file is not compressed |
| contact_email | Email address of this DCC's primary technical contact |
| contact_name | Name of this DCC's primary technical contact |
| creation_time | An ISO 8601 -- RFC 3339 (subset)-compliant timestamp documenting this file's creation time: YYYY-MM-DDTHH:MM:SS±NN:NN |
| data_type | An EDAM CV term ID identifying the type of information stored in this file (e.g. RNA sequence reads): null if is_bundle is set to true |
| dbgap_study_id | The name of a dbGaP study ID governing access control for this file, compatible for comparison to RAS user-level access control metadata |
| dcc_abbreviation | A very short display label for this contact's DCC |
| dcc_description | A human-readable description of this DCC |
| dcc_name | A short, human-readable, machine-read-friendly label for this DCC |
| dcc_url | URL of the front page of the website for this DCC |
| description | A human-readable description of this project |
| disease | A Disease Ontology CV term ID describing this disease |
| ethnicity | A CFDE CV category characterizing the self-reported ethnicity of this subject |
| file_format | An EDAM CV term ID identifying the digital format of this file (e.g. TSV or FASTQ): if this file is compressed, this should be its uncompressed format |
| file_id_namespace | Identifier namespace for this file |
| file_local_id | The ID of this file |
| filename | A filename with no prepended PATH information |
| gene | An Ensembl term ID describing this gene |
| granularity | A CFDE CV category characterizing this subject by multiplicity |
| has_time_series_data | Does this collection contain time-series data? (allowed values: [true |
| id | The identifier for this DCC, issued by the CFDE-CC |
| id_namespace | A CFDE-cleared identifier representing the top-level data space containing this file [part 1 of 2-component composite primary key] |
| local_id | An identifier representing this file, unique within this id_namespace [part 2 of 2-component composite primary key] |
| md5 | (allowed) MD5 checksum for this file [sha256, md5 cannot both be null] |
| mime_type | A MIME type describing this file |
| organism | An NCBI Taxonomy Database ID identifying this gene's source organism (e.g. 'NCBI:txid9606') |
| parent_project_id_namespace | ID of the identifier namespace for the parent in this parent-child project pair |
| parent_project_local_id | The ID of the containing (parent) project |
| persistent_id | A persistent, resolvable (not necessarily retrievable) URI or compact ID permanently attached to this file |
| phenotype | A Human Phenotype Ontology CV term ID describing this phenotype |
| project_id_namespace | The id_namespace of the primary project within which this file was created [part 1 of 2-component composite foreign key] |
| project_local_id | The local_id of the primary project within which this file was created [part 2 of 2-component composite foreign key] |
| protein | A UniProtKB term ID describing this protein |
| race | A race self-identified by this subject |
| role_id | The ID of the role assigned to this organism-level constituent component of this subject |
| sex | A CFDE CV category characterizing the physiological sex of this subject |
| sha256 | (preferred) SHA-256 checksum for this file [sha256, md5 cannot both be null] |
| size_in_bytes | The size of this file in bytes |
| subject_id_namespace | Identifier namespace for this subject |
| subject_local_id | The ID of this subject |
| subset_collection_id_namespace | ID of the identifier namespace corresponding to the C2M2 submission containing the subset collection |
| subset_collection_local_id | The ID of the subset collection |
| substance | A PubChem term ID describing this substance |
| superset_collection_id_namespace | ID of the identifier namespace corresponding to the C2M2 submission containing the superset collection |
| superset_collection_local_id | The ID of the superset collection |
| synonyms | A list of synonyms for this term as identified by the OBI metadata |
| taxon | An NCBI Taxonomy Database ID identifying this taxon |
| taxonomy_id | An NCBI Taxonomy Database ID identifying this taxon |
| uncompressed_size_in_bytes | The total decompressed size in bytes of the contents of this file: null if this file is not compressed |
Enumerations
| Enumeration | Description |
|---|---|
| AssociationTypeEnum | None |
| EthnicityEnum | None |
| GranularityEnum | None |
| RaceEnum | None |
| RoleIdEnum | None |
| SexEnum | None |
Subsets
| Subset | Description |
|---|---|