Search help

Basic search

The simplest way to search is to type a query word/ID into the input box within the mast head and click on the spy glass while the dropdown specifies "Search everything". The default option is a full-text search over all the indexes and fields. If reports are found containing the keyword/ID they are displayed in order of relevance (for more information see indexed fields for each search type). On the left hand side of the results page the filter options (where available) are shown with the numbers of reports associated with each facet.  If the results include gene symbols then clicking on the facet "Gene" will filter the results by this type and will change the faceting to display the locus groups and types that are relevant to the search results; enabling further filtering by locus type. Users can also change the default number of results per page from 10 up to 200.

The results display specific fields from within the search index which differ depending on the document type. The first line of each result contains the gene symbol and the gene name if the result is a gene symbol report, the family name if it's a gene family report or the page title if it hits any other page within the site. The second row will show the type of the indexed document (i.e gene, family or site) if searching everything, and will also contain some of the important fields to help identify the hit. The third row reports the field the keyword/ID matches, so if the keyword matched an approved symbol within a gene symbol report the third row would say "Matches: Gene symbol etc" as seen below in figure 1.

Figure 1: Example of a basic "Search everything" search showing the facets, paging and summarised information.

Advanced search

The search application allows users to make advanced queries using the search box. In this section we describe how to specify the search type, use wildcards, logic operators and specify indexed fields.

Search types

Instead of searching everything, users can select to search only for gene symbol reports, gene families or the static content of the site (e.g. help or news pages) by selecting these options from the dropdown next to the search input box within the mast head.

Wildcard search

Sometimes it may be useful to match records based on a query pattern rather than a keyword or ID. Our search allows users to use wildcard operators with an asterisk (*) to stand in place for one or more characters and a question mark (?) to stand in place for a single character substitution. Multple wildcards can be used in the same query, for instance searching for TP?T* will find the symbol TPST2P1.

Logic operators

By default the search application uses the logical operator OR, so inputing BRAF RNA into the search box actually equates to BRAF OR RNA so some of the results will contain BRAF and some will contain RNA and others may contain both. Sometime however this isn't what a user wants to search. Lets say a user wants to find reports that contain both BRAF and RNA in the same report. Typing in BRAF RNA will unfortunately return over 7000 hits. By changing the search query to BRAF AND RNA the results returned are more pertinent and reduces the number of hits returned. Alternatively asking for reports that do not contain a keyword/ID may be preferable therefore users may use NOT or - within term such as BRAF NOT RNA or BRAF -RNA.

Phrases

As discussed above the default operator is OR, so if a search using the term protein arginine methyltransferase 1 was used the actual search term will be protein OR arginine OR methyltransferase OR 1. This can be addressed by simply quoting the query so that the search knows to treat the quoted block as one term like "protein arginine methyltransferase 1".

Indexed fields

Users may search within a specific indexed field by using the information seen in the indexed fields section below using a very basic notation. To specify an index the user need only to type in to the search field the indexed field key followed immediately with a colon (:) and then the query eg refseq_accession:NM_033360. If the query is not an ID or a keyword "phrases" can be used after the colon eg gene_alias_name:"A-kinase anchor protein, 350kDa".

Indexed fields

"Search everything" fields

ccds_id

Consensus CDS ID. This field may be found within the "NUCLEOTIDE SEQUENCES" section of the gene symbol report e.g. CCDS5863.1

ena

International Nucleotide Sequence Database Collaboration (GenBank, ENA and DDBJ) accession number(s). Found within the "NUCLEOTIDE SEQUENCES" section of the gene symbol report e.g. M95712

ensembl_gene_id

Ensembl gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. ENSG00000157764

entrez_id

Entrez gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. 673

family_alias

Other names used to refer to this family as seen within the gene family reports under the "Also known as" field e.g. LPAAT

family_id

The HGNC gene family ID which can be seen in the URL for a gene family page after the word "set" e.g. 46

family_name

The gene family name as set by the HGNC and seen at the top of the gene family reports e.g. 1-acylglycerol-3-phosphate O-acyltransferases

gene_alias_name

Other names used to refer to this gene as seen in the "SYNONYMS" field in the gene symbol report e.g. A-kinase anchor protein, 350kDa

gene_alias_symbol

Other symbols used to refer to this gene as seen in the "SYNONYMS" field in the gene symbol report e.g. BRAF1

gene_name

HGNC approved name for the gene. Equates to the "APPROVED NAME" field within the gene symbol report e.g. zinc finger protein 536

gene_prev_name

Gene names previously approved by the HGNC for this gene. Equates to the "PREVIOUS SYMBOLS & NAMES" field within the gene symbol report e.g. solute carrier family 5 (choline transporter), member 7

gene_prev_symbol

Gene symbols previously approved by the HGNC for this gene. Equates to the "PREVIOUS SYMBOLS & NAMES" field within the gene symbol report e.g. RN5S49

gene_symbol

The HGNC approved gene symbol. Equates to the "APPROVED SYMBOL" field within the gene symbol report e.g. KLF4

hgnc_id

HGNC ID. A unique ID created by the HGNC for every approved symbol e.g. 1097

locus_group

A group name for a set of related locus types as defined by the HGNC e.g. non-coding RNA.

locus_type

The locus type as set by the HGNC  e.g.RNA, long non-coding

mgd_id

Mouse genome informatics database ID. Found within the "HOMOLOGS" section of the gene symbol report e.g. MGI:88190

page_content

Text contained within the static web page (i.e text within news or help pages) e.g. "human TBX18 gene"

page_title

The title of the static web page (i.e text within news or help pages) e.g. "TBX18 gene therapy"

page_url

The URL of the indexed static web page (i.e text within news or help pages) e.g. hgnc-newsletter-winter-2012-2013

refseq_accession

RefSeq nucleotide accession. This field may be found within the "NUCLEOTIDE SEQUENCES" section of the gene symbol report e.g. NM_033360

rgd_id

Rat genome database gene ID. Found within the "HOMOLOGS" section of the gene symbol report e.g. RGD:2981

rna_central_id

RNAcentral ID. Found within the "NUCLEOTIDE SEQUENCE" section of the gene symbol report e.g. URS000075C808

root_symbol

The common root gene symbol associated to a family if a common root symbol exists.

symbol_status

Status of the symbol report, which can be either "Approved" or "Entry Withdrawn" e.g. Approved

ucsc_id

UCSC gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. uc001rgp.1

uniprot_id

UniProt protein accession. Found within the "PROTEIN RESOURCES" section of the gene symbol report e.g. P00568

vega_id.

Vega gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. OTTHUMG00000020722

"Symbol search" fields

alias_name

Other names used to refer to this gene as seen in the "SYNONYMS" field in the gene symbol report e.g. A-kinase anchor protein, 350kDa

alias_symbol

Other symbols used to refer to this geneas seen in the "SYNONYMS" field in the gene symbol report e.g. BRAF1

ccds_id

Consensus CDS ID. This field may be found within the "NUCLEOTIDE SEQUENCES" section of the gene symbol report e.g. CCDS5863.1

ena

International Nucleotide Sequence Database Collaboration (GenBank, ENA and DDBJ) accession number(s). Found within the "NUCLEOTIDE SEQUENCES" section of the gene symbol report e.g. M95712

ensembl_gene_id

Ensembl gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. ENSG00000157764

entrez_id

Entrez gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. 673

hgnc_id

HGNC ID. A unique ID created by the HGNC for every approved symbol e.g. 1097

locus_group

A group name for a set of related locus types as defined by the HGNC e.g. non-coding RNA

locus_type

The locus type as set by the HGNC e.g. RNA, long non-coding

mgd_id

Mouse genome informatics database ID. Found within the "HOMOLOGS" section of the gene symbol report e.g. MGI:88190

name

HGNC approved name for the gene. Equates to the "APPROVED NAME" field within the gene symbol report e.g. zinc finger protein 536

prev_name

Gene names previously approved by the HGNC for this gene. Equates to the "PREVIOUS SYMBOLS & NAMES" field within the gene symbol report. e.g. solute carrier family 5 (choline transporter), member 7

prev_symbol

Symbols previously approved by the HGNC for this gene. Equates to the "PREVIOUS SYMBOLS & NAMES" field within the gene symbol report e.g. RN5S49

refseq_accession

RefSeq nucleotide accession. This field may be found within the "NUCLEOTIDE SEQUENCES" section of the gene symbol report e.g. NM_033360

rgd_id

Rat genome database gene ID. Found within the "HOMOLOGS" section of the gene symbol report e.g. RGD:2981

rna_central_id

RNAcentral ID. Found within the "NUCLEOTIDE SEQUENCE" section of the gene symbol report e.g. URS000075C808

status

HGNC status for gene symbol reports the values of which will either be "Approved" or "Entry Withdrawn" e.g. Approved

symbol

The HGNC approved gene symbol. Equates to the "APPROVED SYMBOL" field within the gene symbol report e.g. KLF4

ucsc_id

UCSC gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. uc001rgp.1

uniprot_ids

UniProt protein accession. Found within the "PROTEIN RESOURCES" section of the gene symbol report e.g. P00568

vega_id

Vega gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. OTTHUMG00000020722

"Gene family search" fields

family_alias

Other names used to refer to this family as seen within the gene family reports under the "Also known as" field e.g. LPAAT

family_id

The HGNC gene family ID which can be seen in the URL for a gene family page after the word "set" e.g. 46

family_name

The gene family name as set by the HGNC and seen at the top of the gene family reports e.g. 1-acylglycerol-3-phosphate O-acyltransferases

gene_alias_name

Other names used to refer to a gene associated with the family and seen in the "SYNONYMS" field in the gene symbol report e.g. lysophosphatidic acid acyltransferase, beta

gene_alias_symbol

Other symbols used to refer to a gene associated with the family and  seen in the "SYNONYMS" field in the gene symbol report e.g. MAG1

gene_name

HGNC approved name for a gene associated with the family and equates to the "APPROVED NAME" field within the gene symbol report e.g. zinc finger protein 536

gene_prev_name

Gene names previously approved by the HGNC for genes associated with the gene family and equates to the "PREVIOUS SYMBOLS & NAMES" field within the gene symbol report e.g. Berardinelli-Seip congenital lipodystrophy

gene_prev_symbol

Gene symbols previously approved by the HGNC for genes associated with the gene family and equates to the "PREVIOUS SYMBOLS & NAMES" field within the gene symbol report e.g. BSCL

gene_symbol

The HGNC approved gene symbol for a gene associated to the gene family and equates to the "APPROVED SYMBOL" field within the gene symbol report e.g. AGPAT1

hgnc_id

HGNC ID. A unique ID created by the HGNC for every approved symbol e.g. HGNC:324

root_symbol

The common root gene symbol associated to a family if a common root symbol exists e.g. AGPAT

"Site search" fields

page_content

Text contained within a static web page (i.e text within news or help pages) e.g. "human TBX18 gene"

page_title

The title of a static web page (i.e text within news or help pages) e.g. "TBX18 gene therapy"

page_url

The URL of an indexed static web page (i.e text within news or help pages) e.g. hgnc-newsletter-winter-2012-2013