Using the Bioscape Web Application

The Bioscape Web application seeks to provide a convenient interface to textual documents which have been searched for bioentity (gene and/or protein) information, as well as providing an overview of each bioentity known to the system.

Searching

The start page for Bioscape provides a minimal search dialogue where names or identifiers of bioentities can be specified, together with the kind of bioentity being searched for, and along with any organism-related restrictions. Upon searching (by pressing the Go! button), if only a single gene satisfies the search criteria, a summary page will be shown for that gene; otherwise, a disambiguation page will be shown first, as described below.

Searching for Genes by Name

An example:

1. Enter LHbeta into the text box.
2. Select name from the input type menu.
3. Select either human or all organisms from the organism menu, according to preference.
4. Press the Go! button.

Bioscape will not only attempt to match the given name against the names recorded for genes in typical gene databases, but it will also attempt to suggest genes that are thought to employ the given name in the searched literature. Consequently, for the above example, genes known by the names LH2 and LHB will be suggested. (This depends on a technique known as orthographic variation.)

Searching for Genes by Identifier

An example:

1. Enter 1234 into the text box.
2. Select Entrez Gene identifier from the input type menu.
3. Select either human or all organisms from the organism menu, according to preference.
4. Press the Go! button.

Bioscape will attempt to show a summary page for the chosen gene. If the chosen organism is not compatible with the gene whose identifier has been given, or if no such identifier is known, an error will be shown.

Searching for Genes via Protein Accessions

An example:

1. Enter NP_001099006.1 into the text box.
2. Select RefSeq protein accession from the input type menu.
3. Select either human or all organisms from the organism menu, according to preference.
4. Press the Go! button.

Bioscape will attempt to show the summary page for the gene associated with the specified product.

Search Disambiguation

When Bioscape cannot be sure which gene whose details the user wishes to investigate, a disambiguation page will appear and the user will be requested to choose one of a number of suggestions.

An example:

1. First, search for LHbeta as a name in human (as described above).
2. A number of suggestions are proposed for genes in which the user might be interested.
3. Press the Go! button next to the gene which is most appropriate, such as LH2 ("luteinizing hormone beta polypeptide", Entrez Gene #3972).

Gene Summaries

Each gene summary contains the following sections:

• Basic information about the gene.
• A list of protein products associated with the gene.
• A list of names by which the gene is known.
• A list of co-occurrences showing, for the featured gene, those genes which appear together with the gene in sentences in the literature.

From most sections, a Go! button is provided which leads to textual results showing "mention sentences" involving the gene:

• From the basic information, textual results show any mention of the gene under any name.
• From the list of names, textual results show only mentions of the gene using the corresponding specific name.
• From the list of co-occurrences, textual results show any co-occurring mention of the two genes concerned (the featured gene and that given in the list) under any of their names.

Mention Sentences

The following kinds of mention sentence pages are provided in Bioscape:

• Mentions of a gene under any name.
• Mentions of a gene using a specific name.
• Mentions of a gene appearing together with another specified gene, for any known name employed by either gene.

In all such pages, a list of sentences grouped by document are shown, and the following features are provided:

• For each document, a header shows the source of the document, providing a link to the complete document summary and a link to a list of document versions (described below).
• Each document provides a number of sentences featuring the gene as described above. Each mention is highlighted showing elementary details of the mention; for more details the complete document summary should be visited.