Bioscape Methods
Please note that this documentation covers an unreleased product and is for internal use only.
This document describes the role of methods in Bioscape.
Contents
Processing, Methods and Scoring
The processing pipeline of Bioscape can be summarised as follows:
- Import information about biological entities (genes, proteins), also known as bioentities.
- Build a lexicon consisting of names associated with the imported entities as well as more general terms associated with other kinds of data.
- Search biomedical literature using the contents of the lexicon, subject to filtering.
- Assign bioentities to the text search results.
At each stage in the pipeline, Bioscape employs methods which are used to assess the value or suitability of the information employed by assigning scores to the information based on particular criteria. Consequently, the following kinds of methods are applied:
- Term scoring: assessing whether a term (or name) should be used in text searches.
- Search scoring: assessing whether a bioentity should be assigned to a text search result.
- Sentence scoring: assessing whether a sentence has a particular importance.
- Result scoring: assessing whether a result (combining bioentity and textual information) is genuine.
Examples of methods are given below.
Name Scoring
Search Scoring
Sentence Scoring
Result Scoring
The scoring of results involves inspecting the proposed bioentities and assessing their suitability in a particular document location. Such assessment methods employ the following approaches:
| Effect of method | ||
| Means of assessment | Confirm bioentity relevance (scoring supported bioentities positively) | Disambiguate bioentities (identifying unsupported bioentities and scoring them negatively) |
| Find supporting contextual information | ||
| Find more supporting contextual information for the "best" bioentities | ||
| Compare bioentities in order to identify the "best" bioentities | ||
Methods which confirm bioentity relevance may be combined to test whether a mention satisfies the criteria from all such methods. However, where a mention need only satisfy the criteria from a single method, it is more appropriate to combine disambiguation methods, since these should only exclude mentions on a conservative basis.
Competing Names
PubMed #7479798: gene #1434 is referenced by names CSE1 and CAS, but CAS is used ambiguously. Since the other genes referenced by CAS are not supported by other names, CAS is interpreted as also being a reference to gene #1434.
