Welcome to the LiverCancerMarkerRIF project

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Motivation and Background

Entrez Gene is a repository for gene-specific knowledge of the National Center for Biotechnology Information (NCBI). In addition to general and genomic information, narrative evidences regarding the gene functions within publications can be found in the GeneRIF (Gene Reference Into Function) section. This section provides a platform that enables scientists to share and enrich gene-related functional annotations.

In view of GeneRIF, we developed a browser extension named "LiverCancerMarkerRIF", which allows users to view and edit gene-related functions related to liver cancer described in the abstract instantly online. Replacement of the word “Gene” with “Marker” delivers the main purpose of our tool, which is to look for supporting evidence of liver cancer biomarker candidates that were uncovered through previous text-mining processes.

LiverCancerMarkerRIF contains functions including the recognition of gene, disease, post-translational modifications, mutations and investigative technologies, linking of the aforementioned terms to their corresponding database, and the extraction of LiverCancerMarkerRIF sentences. Furthermore, a user curation interface is available to submit suggestions on the sentences extracted. Once confirmed, users can directly submit the function-describing sentence to our LiverCancerMarkerRIF database.

A collection of this knowledge from the literature should provide additional help in the study of biomarkers and may supplement clinical decision making.

System Description/Curation Guideline

Download

Please follow the following two links to download the LiverCancerMarkerRIF extension for

TIPS: Right click one of the above link and choose "save as..." to download our extension

Default marker list file: Default.txt

Proposed tasks and curators for the IAT track for MarkerRIF

When given a list of genes related to a specific disease:

  1. Search PubMed using the predefined query terms, and identify whether the abstracts contain disease biomarker-related information (curatable abstracts).
  2. As for curatable abstracts, extract the following information: PMID of the abstract, gene terms and its corresponding gene ID from Entrez Gene, evidence sentence containing RIF information, and relation assertion (descriptive of RIF or not).
The task will be run both manually and using MarkerRIF.
  • Manual task: Curators will be given a list of PubMed abstracts for further processing, and should provide an output spreadsheet that contains the information of interest.
  • Using MarkerRIF: Curators will compare the information retrieved by MarkerRIF regarding the given set of abstracts with those that are extracted manually, analyze their differences and offer suggestions for further improvement.

Pre-defined Query Terms

	(((((blood[Title/Abstract]) OR serum[Title/Abstract]) OR urine[Title/Abstract]) AND clinical[Title/Abstract]) OR diagnosis[Title/Abstract]) AND liver cancer[Title/Abstract]