BioGene 1.1 – Information Tool for Biological Research for Iphone
From the website:
BioGene is an information tool for biological research. Use BioGene to learn about gene function. Enter a gene symbol or gene name, for example “CDK4″ or “cyclin dependent kinase 4″ and BioGene will retrieve its gene function and references into its function (GeneRIF).
The search/match criteria of Biogene is instructive:
Where does BioGene get its data? BioGene provides primary information from Entrez Gene, a searchable database hosted by the NCBI. What is a GeneRIF? A GeneRIF is a functional annotation of a gene described in Entrez Gene. The annotation includes a link to a citation within PubMed which describes the function. Please see GeneRIF for more information. How does BioGene search Entrez Gene? BioGene attempts to match a query against a gene name (symbol). If no matching records are found, BioGene applies mild increments in permissiveness until a match is found. For example, if we are searching for the following single-term query, “trk”, BioGene will attempt the following sequence of queries in succession, stopping whenever one or more matching records is returned:
- search for a gene name (symbol) that matches the exact sequence of characters “trk”
- search for a gene name (symbol) that starts with the sequence of characters “trk”
- search for a gene name (symbol) that contains the sequence of characters “trk” within a word
- perform a free text search that matches the exact sequence of characters “trk”
- perform a free text search that starts with the sequence of characters “trk”
- perform a free text search that contains the sequence of characters “trk” within a word
In Entrez Gene parlance, for the following single-term query “trk”, the following sequence of queries is attempted:
- trk[pref]
- trk*[pref] OR trk[sym]
- trk*[sym]
- *trk*[sym]
- trk[All Fields]
- trk*[All Fields]
- *trk*[All Fields]
If however, we are searching for the following multi-term query, “protein kinase 4”, BioGene will attempt the following sequence of queries in succession, stopping whenever one or more matching records is returned:
- search for a full gene name that matches the exact sequence of characters “protein kinase 4”
- perform a free text search that contains every term in the multi-term query “protein kinase 4”
- perform a free text search that contains one of the terms in the multi-term query “protein kinase 4”
In Entrez Gene parlance, for the following multi-term query “protein kinase 4”, the following sequence of queries is attempted:
- protein+kinase+4[gene full name]
- protein[All Fields] OR kinase[All Fields] OR 4[All Fields]
If BioGene detects one or more of the following character sequences within the query:
[ ] * AND OR NOT it treats this as an “advanced” query and passes the query directly to Entrez Gene. In this situation, BioGene ignores the organism filter specified in the application settings and expects the user to embed this filter within the query.
BioGene gives you access to subjects by multiple identifiers and at least for a closed set of data, attempts to find a “best” match.
Review Entrez Gene.
What other identifiers suggest themselves as bases of integrating known sources of additional information?
(Only “known” sources can be meaningfully displayed/integrated for the user.)