LocusLink
Please Note: As of July 1st, 2005 the NCBI is no longer updating Locuslink.
- LocusLink
comes from the National Center for Biotechnology Information, and is
described by its creators thusly:
- LocusLink provides a single query interface to curated sequence
and descriptive information about genetic loci. It presents
information on official nomenclature, aliases, sequence accessions,
phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map
locations, and related web sites.
- The current scope is fruit fly, human, human immunodeficiency
virus type 1, mouse, rat, and zebrafish.
- [online; accessed 11/13/02; http://www.ncbi.nlm.nih.gov/LocusLink/]
Schema in CLSD
LocusLink tables are found under the 'locuslink' schema.
| Table | Field | Type | Description |
|---|
| PHENOTYPE |
LOCUS_ID | BIGINT | |
| PHENOTYPE | VARCHAR(124) | |
| PHENOTYPE_ID | BIGINT | |
| GENBANK_SEQUENCES |
LOCUS_ID | BIGINT | |
| NUCLEOTIDE | VARCHAR(16) | |
| TYPE | CHAR(1) | |
| PROTEIN | VARCHAR(8) | |
| ALIAS_PROTEINS |
LOCUS_ID | BIGINT | |
| ALIAS | VARCHAR(200) | |
| MODEL |
LOCUS_ID | BIGINT | |
| EVIDENCE | VARCHAR(256) | |
| MRNA_ACCESSION | CHAR(9) | |
| PROTEIN_ACCESSION | CHAR(9) | |
| CHROMOSOME |
LOCUS_ID | BIGINT | |
| CHROMOSOME_ID | VARCHAR(24) | |
| MODEL_REFSEQ_ACCESSION |
LOCUS_ID | BIGINT | |
| PROTEIN | CHAR(13) | |
| PID | BIGINT | |
| LINKS |
LOCUS_ID | BIGINT | |
| URL | VARCHAR(200) | |
| REFSEQ |
LOCUS_ID | BIGINT | |
| MRNA | CHAR(9) | |
| PROTEIN | CHAR(9) | |
| PRODUCT | VARCHAR(210) | |
| GENBANK_SOURCE | VARCHAR(64) | |
| MAP |
LOCUS_ID | BIGINT | |
| CYTOGENETIC_LOCATION | VARCHAR(128) | |
| SOURCE | VARCHAR(256) | |
| TYPE | CHAR(1) | |
| STS_MARKERS |
LOCUS_ID | BIGINT | |
| NAME | VARCHAR(30) | |
| CHROMOSOME | VARCHAR(3) | |
| STS_ID | BIGINT | |
| D_SEGMENT | VARCHAR(16) | |
| SEQ_KNOWN | VARCHAR(16) | |
| EVIDENCE | VARCHAR(64) | |
| LOCI |
LOCUS_ID | BIGINT | |
| ORGANISM | VARCHAR(45) | |
| SYMBOL | VARCHAR(50) | |
| PRODUCT | VARCHAR(200) | |
| TYPE | VARCHAR(128) | |
| NAME_TYPE | CHAR(1) | '0' or 'P'. Determines whether the information in the SYMBOL and PRODUCT fields refer to OFFICIAL or PREFERRED symbols and gene names. |
| ALIAS_SYMBOLS |
LOCUS_ID | BIGINT | |
| ALIAS | VARCHAR(128) | |
| GO |
LOCUS_ID | BIGINT | |
| CATEGORY | VARCHAR(24) | |
| TERM | VARCHAR(120) | |
| EVIDENCE_CODE | CHAR(16) | |
| IDENTIFIER | VARCHAR(16) | |
| ANNOTATION_SOURCE | VARCHAR(16) | |
| GO_PUBMED_ID |
LOCUS_ID | BIGINT | |
| PUBMED_ID | VARCHAR(16) | |
| EXTANNOT |
LOCUS_ID | BIGINT | |
| TERM_CATEGORY | VARCHAR(32) | |
| TERM | VARCHAR(64) | |
| EVIDENCE_CODE | VARCHAR(16) | |
| ANNOTATION_SOURCE | VARCHAR(16) | |
| PUBMED_ID | VARCHAR(8) | |
| CONTIG |
LOCUS_ID | BIGINT | |
| ACCESSION | VARCHAR(32) | |
| GI_NUM | BIGINT | |
| STRAIN | VARCHAR(32) | |
| START | BIGINT | |
| END | BIGINT | |
| ORIENTATION | CHAR(1) | |
| SOURCE | VARCHAR(32) | |
| REFSEQ_ACCESSION |
LOCUS_ID | BIGINT | |
| PROTEIN | CHAR(9) | |
| PID | BIGINT | |
| TRANSCRIPT_VARIANT |
LOCUS_ID | BIGINT | |
| VARIANT | VARCHAR(725) | |
| ECNUM |
LOCUS_ID | BIGINT | |
| ECNUM | VARCHAR(64) | |
| SUMMARY |
LOCUS_ID | BIGINT | |
| SUMMARY | VARCHAR(9999) | |
