PubPularDB and FaBian Updates
Similar Posts
Mass Spectrometer Delivered! Sun 20 Aug 2017 |
We acquired a Thermo Q-Exactive HF mass spectrometry, …
BioArXiV article on Gene Annotation Bias Fri 20 Oct 2017 |
We previously published a data science method PubPular …
Quantifying the value of basic science Thu 07 Sep 2017 |
In this era of constrained research funding, the …
Lab receives 5-year R01 funding Sat 02 Jun 2018 |
We are excited to receive a generous 5-year …
Popular protein manuscript released on bioRxiv Tue 25 Sep 2018 |
Our manuscript on popular proteins across the human …
Alternative splice isoform companion data on website Sat 11 Apr 2020 |
We recently published our study on finding protein …
What does oxidative stress do to the heart? Examining proteomic changes Mon 01 Jun 2020 |
The heart is an organ that is very …
Recent publications October 2020 Fri 30 Oct 2020 |
Check out some recent publications from our team …
Combining machine learning and targeted mass spectrometry to validate protein isoforms Tue 16 Feb 2021 |
Why identify protein isoforms?Alternative splicing plays a very …
Sept. 6, 2017, 3:14 a.m.
Maggie-Lam
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
