PubPularDB and FaBian Updates

Bioinformatics Proteomics

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Our lab recently received funding from the NIH Common Funds Cloud Credit Model Pilot Program for our bioinformatics project and web app Pubpular.

The NIH Cloud Credits Model is a new component within the NIH Big Data to Knowledge (BD2K) program that gives out pre-paid credits for accessing cloud technologies in NIH-supported research. More information can be found on the NIH Common Funds website.

With the help of the cloud credits we will be able to move Pubpular to a new web host shortly and also implement a planed functionality of the web app called Fabian (Functional Annotation via Bibliometrics Analysis). Currently the Pubpular web app allows users to calculate the normalized co-publication distance of genes and proteins of interest with research article in user-defined topics. We have previously shown that this metric is useful for identifying popular and relevant proteins in a research fields that may be considered prioritized candidates for clinical translation.

Coinciding with the funding decision, we have also pushed a major update on Pubpular. The new PubpularDB component contains pre-calculated NPDs for over 17,000 genes in the human genomes with a large collection of disease and phenotype terms in defined vocabularies and ontologies. This includes over 5,000 terms from BRENDA Tissue Ontology, and over 9,000 terms from Disease Ontology. The new Fabian component will be powered by PubpularDB, and allow users to upload and analyze gene lists for similarities to curated search terms in each vocabulary.

The technical details of PubPular and NPD can be found in our publications on Journal of Proteome Research.

Image Credit: João Silas