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Entrez Help Document |
| PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure |
Last modified : July 18, 2000
| Databases | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Limits | Nucleotide | Protein | Genome | Structure | PopSet | ||||||
| Search Fields | Yes | Yes | Yes | Yes | Yes | ||||||
| Exclude ESTs | Yes | No | No | No | No | ||||||
| Exclude STSs | Yes | No | No | No | No | ||||||
| Exclude GSSs | Yes | No | No | No | No | ||||||
| Exclude Working Draft | Yes | No | No | No | No | ||||||
| Exclude Patents | Yes | Yes | No | No | No | ||||||
| Molecule Type | Yes | No | No | No | No | ||||||
| Gene Location | Yes | Yes | No | No | No | ||||||
| Segmented Sequences | Yes | Yes | No | No | No | ||||||
| Database Source | Yes | Yes | No | No | No | ||||||
| Modification Date | Yes | Yes | No | No | No | ||||||
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| Databases | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Search Field Descriptions and Qualifiers | Nucleotide | Protein | Genome | Structure | PopSet | ||||||
| Accession | Yes | Yes | Yes | Yes | Yes | ||||||
| All Fields | Yes | Yes | Yes | Yes | Yes | ||||||
| Author Name | Yes | Yes | Yes | Yes | Yes | ||||||
| EC/RN Number | Yes | Yes | Yes | Yes | Yes | ||||||
| Feature Key | Yes | No | Yes | No | Yes | ||||||
| Filter | Yes | Yes | Yes | Yes | Yes | ||||||
| Gene Name | Yes | Yes | Yes | No | Yes | ||||||
| Issue | Yes | Yes | Yes | Yes | Yes | ||||||
| Journal Name | Yes | Yes | Yes | Yes | Yes | ||||||
| Keyword | Yes | Yes | Yes | No | Yes | ||||||
| Modification Date | Yes | Yes | Yes | Yes | Yes | ||||||
| Molecular Weight | No | Yes | No | No | No | ||||||
| Organism | Yes | Yes | Yes | Yes | Yes | ||||||
| Page Number | Yes | Yes | Yes | Yes | Yes | ||||||
| Primary Accession | Yes | Yes | Yes | No | Yes | ||||||
| Properties | Yes | Yes | Yes | No | Yes | ||||||
| Protein Name | Yes | Yes | Yes | No | Yes | ||||||
| Publication Date | Yes | Yes | Yes | Yes | Yes | ||||||
| SeqID String | Yes | Yes | Yes | No | Yes | ||||||
| Sequence Length | Yes | Yes | Yes | No | No | ||||||
| Substance Name | Yes | Yes | No | Yes | No | ||||||
| Text Word | Yes | Yes | Yes | Yes | Yes | ||||||
| Title Word | Yes | Yes | Yes | No | No | ||||||
| Uid | No | No | No | No | No | ||||||
| Volume | Yes | Yes | Yes | Yes | Yes | ||||||
| Search Field | Definition | Qualifier | |||
|---|---|---|---|---|---|
| Accession | Contains the unique accession number of the sequence or record, assigned to the nucleotide, protein, structure, genome record, or PopSet by a sequence database builder. The Structure database accession index contains the PDB IDs but not the MMDB IDs. | [ACCN] | |||
| All Fields | Contains all terms from all searchable database fields in the database. | [ALL] | |||
| Author Name | Contains all authors from all references in the database records. The format is last name space first initial(s), without punctuation (e.g., marley jf). | [AUTH] | |||
| EC/RN Number | Number assigned by the Enzyme Commission or Chemical Abstract Service (CAS) to designate a particular enzyme or chemical, respectively. | [ECNO] | |||
| Feature Key | Contains the biological features assigned or annotated to the nucleotide sequences and defined in the DDBJ/EMBL/GenBank Feature Table (http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html). Not available for the Protein or Structure databases. | [FKEY] | |||
| Filter | Contains predetermined or filtered subsets of the various databases. These
subsets or filters are created by grouping records that are commonly linked
to other Entrez databases or within the same database. For example, the PopSet database Filter index includes PopSet all, PopSet medline, PopSet nucleotide, and PopSet protein. The PopSet medline filter includes all PopSet records with links to PubMed; the PopSet nucleotide filter includes all PopSet records with links to the nucleotide database; and, the PopSet protein filter includes all PopSet records with links to the protein database. The PopSet all filter includes all PopSet records. The Nucleotide database Filter index contains a great deal more filters because the database records are linked to numerous external links. For more information see Link Out. |
[FILT] | |||
| Gene Name | Contains the standard and common names of genes found in the database records. This field is not available in Structure database. | [GENE] | |||
| Issue | Contains the issue number of the journal in which the data were published. | [ISS] | |||
| Journal Name | Contains the name of the journal in which the data were published. Journal names are indexed in the database in abbreviated form (e.g., J Biol Chem). Journals are also indexed by their by ISSNs. Browse the index if you do not know the ISSN or are not sure how a particular journal name is abbreviated. | [JOUR] | |||
| Keyword | Contains special index terms from the controlled vocabularies associated with the GenBank, EMBL, DDBJ, SWISS-Prot, PIR, PRF, or PDB databases. Browse the Keyword indexes of the individual databases to become familiar with these vocabularies. A Keyword index is not available in the Structure database. | [KYWD] | |||
| Modification Date | Contains the date that the most recent modification to that record is indexed in Entrez, in the format YYYY/MM/DD (e.g., 1999/08/05). A year alone, (e.g., 1999) will retrieve all records modified for that year; a year and month (e.g., 1999/03) retrieves all records modified for that month that are indexed in Entrez. | [MDAT] | |||
| Molecular Weight | Molecular weight of a protein, in Daltons (Da), calculated by the method described in the Searching by Molecular Weight section of the Entrez help document. Note that molecular weight must be entered as a fixed 6 digit field, filled with leading zeros (not letter O), e.g., 002002 [MOLWT] | [MOLWT] | |||
| Organism | Contains the scientific and common names for the organisms associated with protein and nucleotide sequences. | [ORGN] | |||
| Page Number | Contains the number of the first journal page of the article in which the data were published. | [PAGE] | |||
| Primary Accession | Contains the primary accession number of the sequence or record, assigned to the nucleotide, protein, structure, genome record, or PopSet by a sequence database builder. A Primary Accession index is not available in the Structure database. | [PACC] | |||
| Properties | Contains properties of the nucleotide or protein sequence. For example, the Nucleotide database's Properties index includes molecule types, publication status, molecule locations, and GenBank divisions. A Properties index is not available in the Structure database. | [PROP] | |||
| Protein Name | Contains the standard names of proteins found in database records. Common names may not be indexed in this field so it is best to also consider All Fields or Text Words. A Protein Name index is not available in the Structure database. | [PROT] | |||
| Publication Date | Contains the date that records are released into Entrez, in the format YYYY/MM/DD (e.g., 1999/08/05). It is the date the entry first appeared in GenBank explicitly indexed in Entrez. A year alone, (e.g., 1999) will retrieve all records for that year; a year and month (e.g., 1999/03) will retrieve all records released into GenBank for that month. | [PDAT] | |||
| SeqID String | Contains the special string identifier, similar to a FASTA identifier, for a given sequence. A SeqID String index is not available in the Structure database. | [SQID] | |||
| Sequence Length | Contains the total length of the sequence. Sequence Length indexes are not available in the Structure or PopSet databases. | [SLEN] | |||
| Substance Name | Contains the names of any chemicals associated with this record from the CAS registry and the MEDLINE Name of Substance field. Substance Name indexes are not available in the Genome or PopSet databases. | [SUBS] | |||
| Text Word | Contains all of the "free text" associated with a record. | [WORD] | |||
| Title Word | Includes only those words found in the definition line of a record. The definition line summarizes the biology of the sequence and is carefully constructed by database staff. A standard definition line will include the organism, product name, gene symbol, molecule type and whether it is a partial or complete cds. Title Word indexes are not available in the Structure or PopSet databases. | [TITL] | |||
| Uid | Contains the Medline unique identifier for records that contain published references that are linked to PubMed. The Uid index is not browsable. | [UID] | |||
| Volume | Contains the volume number of the journal in which the data were published. | [VOL] | |||
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| Display Format | Description | Databases Available | Link | ||||
|---|---|---|---|---|---|---|---|
| Summary | Default display, hotlinked Accession number and brief description | All databases | None | ||||
| Brief | Hotlinked Accession number and abbreviated description | All databases | None | ||||
| GenBank/GenPept | Full report format | Nucleotide, Protein | None | ||||
| ASN.1 | Abstract Syntax Notation 1 form, the computer-readable form of the data | All databases | None | ||||
| FASTA | The definition line and sequence characters | All databases | None | ||||
| Nucleotide Neighbors | Retrieves all similar nucleotide sequences for all documents retrieved and displays in default format | Nucleotide | Related Sequences | ||||
| Protein Neighbors | Retrieves all similar protein sequences for all documents retrieved and displays in default format | Protein | Related Sequences | ||||
| Genome Neighbors | Retrieves all similar genome sequences for all documents retrieved and displays in default format | Genome | Related Sequences | ||||
| Structure Neighbors | Retrieves all similar structures for all documents retrieved and displays in default format | Structure | Related Sequences | ||||
| Provider Links | Retrieves all external links for all documents retrieved and displays in default format - see Link Out for more information | All databases | LinkOut | ||||
| PubMed Links | Retrieves all Medline links for all documents retrieved and displays in default format | All databases | PubMed | ||||
| Nucleotide Links | Retrieves all Nucleotide links for all documents retrieved and displays in default format | All databases, except Nucleotide | Nucleotide | ||||
| Protein Links | Retrieves all Protein links for all documents retrieved and displays in default format | All databases, except Protein | Protein | ||||
| Genome Links | Retrieves all Genome links for all documents retrieved and displays in default format | Nucleotide, Protein, and Structure | Genomes | ||||
| Structure Links | Retrieves all Structure links for all documents retrieved and displays in default format | Nucleotide, Protein, and Genome | Structure | ||||
| PopSet Links | Retrieves all PopSet links for all documents retrieved and displays in default format | All databases | PopSet | ||||
| Graphic Summary | The graphical view of the sequence accessible by selecting the hotlinked Accession numbers | Nucleotide, Protein, and Genome | None | ||||
| Structure Summary | The Structure Summary accessible by selecting the hotlinked PDB numbers | Structure | None | ||||
| PopSet Summary | The complete set of Accession Numbers comprising the PopSet accessible by selecting the hotlinked PopSet Accession Numbers | PopSet | None | ||||
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