GNF Malaria Literature Web Portal
How to Access the Web Portal
Visit http://carrier.gnf.org/publications/Py, then follow the "Literature Database" link. This is an open-access web site.
What is the Malaria Literature Database
The main source of gene annotation currently comes from gene
ontology (GO, http://geneontology.org). However, there are not as much resource
devoted to manual curation of GO annotations compared to other model
organisms. Incomplete gene annotation slows down malaria
research. Literature searches in
NCBI PubMed can lead to interesting information, however, the system only
indexes paper title and abstract. The
body text of a paper is not indexed in both PubMed and PubMed Central. As more and more open-access
publications become available, search for the occurrence of a gene name inside
the body of a paper becomes feasible using services such as Google Scholar (http://scholar.google.com) and Scirus (http://www.scirus.com/srsapp/)
systems. At the time of our
exercise, MAL13P1.119 has no hit
either in PubMed or PMC, but there are two different journal hits, one in
Google Scholar, another in Scirus. We here collect gene name-publication pairs using these
two Internet search engines, where P.
yoelii and both old and new P.
falciparum locus names were used as search terms. We also make use of NCBI GenBank-PubMed
links for P. falciparum, P. yoelii, P.
bergeii, and P. chaubaudi, the result is a relatively comprehensive gene-literature
database. The open-access web
portal should provide easier access to the database and facilitate malaria researchers
in gene function annotation.
Note: One caveat is search
engines do not seem to index supplementary materials. Even they do, it will be
difficult to map those hits back to the original PubMed ID.
Key Web Components and Linkages
Start your search from the overview page with gene or paper
terms. Search results can direct you to either "Gene Table View" or
"Paper Table View". Clicking on 
icon opens the "Gene Report".
Each gene is linked to a "Paper Table View" containing all the papers
it is cited by. Each paper is linked to a "Gene Table View"
containing all its gene members.
How to Search for Genes and Papers
Enter gene locus name (e.g., PFI1445w), or PubMed ID (e.g., 16497586). Keywords in gene descriptions or paper title can also be searched (e.g., motility or "ookinete invasion").
Different types of search terms can be entered together and the "Search" program has the intelligence of distinguishing what is a locus name, a PubMed ID, or just a general keyword. Click the "Example" button, then the "Search" button to check what the search engine can accommodate.
You can click any of the number links on the overview page
to browse either genes or papers in their "Table View".
How to Make Use of the Search Result Page
Search results may contain both paper entries and gene entries.
Each paper entry is displayed with a 
icon that links to NCBI PubMed, as
well as a 
icon that will display all the genes in
that paper in the "Gene Table" view.
Each gene entry is displayed with a link to PlasmoDB, gene names are linked to the "Gene Report" page, where all information about the gene is listed.
What is Contained in the Gene Report Page
Gene report page contains all the details about the gene. It starts with key statistical information, followed by its orthologs, then all the papers the gene is cited, and all other genes co-cited in each paper.
What is Contained in the "Gene Table" View
"Gene Table" view is an Excel-like web interface to browse a list of genes. The web page contains many useful features as shown in the snapshot below.
What is Contained in the "Paper Table" View
"Paper Table" view is an Excel-like web interface to browse a list of papers. The web page contains many useful features as shown in the snapshot below.
Download All Data in Batch
All data are available for download from our paper companion web site: http://carrier.gnf.org/publications/Py, Table S3-S4 and an additional CSV file for PMID:15591202.
Contact Us
Please email zhou at gnf dot org