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Detailed information about post-translational modification (PTM) terms
The ptm.tsv table will have as many rows as the number of unique PTM terms appearing in the ptm column of biosample_ptm.tsv and collection_ptm
| Field | Field Description | Required? | Field Value Type | Extra Info |
|---|---|---|---|---|
| id | A unique PTM ID. [Primary key] | Required | string | This ID should be unique across DCCs. One way is to use the MD5 hash value of the concatenated string of the remaining columns (including the optional columns). |
| protein | A UniProt Knowledgebase (UniProtKB) protein accession (AC) | Required | string (Valid Term) | Example: P14210-1 |
| site_one | The position of the first site involved in the PTM or the start site in a peptide range. | Required | Positive integers or (empty) | Example: 178 |
| aa_site_one | The amino acid at the first site | Required | Single letter code of AA or (empty) | Example: N |
| site_two | The position of the second site involved in the PTM or the end site/an alternate site in a peptide range. For the exact position, this will be empty. | Optional | Positive integers or (empty) | Example: 199 |
| aa_site_two | The amino acid at the second site | Optional | Single letter code of AA or (empty) | Example: S |
| site_type | Type of site, a valid site_type term ID from the CV table site_type.tsv | Optional | String, one of {defined;range;alternative;connect;unknown} | Example: defined. This will be the value in the id column in the row in the CV table site_type.tsv corresponding to the site_type for this PTM, although no formal foreign key constraint is imposed. |
| ptm_type | Major type of PTM, a valid ptm_type ID | Optional | Gene Ontology ID | Example: GO:0006486. Foreign key: It is the value at column id in the table ptm_type.tsv corresponding to this ptm_type. |
| ptm_subtype | Subtype of PTM, a valid ptm_subtype ID | Optional | Gene Ontology ID | Example: GO:0006493. Foreign key: It is the value at column id in the table ptm_subtype.tsv corresponding to this ptm_subtype. |
| domain_location | ID for subcellular localization | Optional | Gene Ontology ID | Example: GO:0005634. Foreign key: this will be the value in the id column in the row in the table domain_location.tsv corresponding to the domain_location for this PTM. |
| domain_type | Domain type | Optional | string | Example: Src homology 3 (SH3) domain |