Search help

Our search options allow users to search all of our active gene symbol reports quickly and with ease. The search server utilises Apache Solr which offers a powerful full-text search, hit highlighting and faceted searching. Faceted searching allows you to search for a particular keyword and then filter the results by record/page type, locus group and locus type.

The search form can be found within the mast head of each page. Enter a search term within the search input box and click on the spy glass icon.

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. If reports are found containing the keyword/ID they are displayed in order of relevance (for more information see indexed fields). 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. The first line of each result contains the gene symbol and the gene name. The second row will show 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".

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.

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

"Symbol search" fields

ensembl_gene_id
Ensembl gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. ENSPTRG00000017914
NCBI gene id
NCBI gene ID. Found within the "GENE RESOURCES" section of the gene symbol report e.g. 455683
vgnc_id
VGNC ID. A unique ID created by the VGNC for every approved symbol e.g. 1097
locus_group
A group name for a set of related locus types as defined by the VGNC e.g. protein-coding gene
locus_type
The locus type as set by the HGNC e.g. gene with protein product
name
VGNC approved name for the gene. Equates to the "APPROVED NAME" field within the gene symbol report e.g. zinc finger protein 536
status
VGNC status for gene symbol reports the values of which will either be "Approved" or "Entry Withdrawn" e.g. Approved
symbol
The VGNC approved gene symbol. Equates to the "APPROVED SYMBOL" field within the gene symbol report e.g. UTRN