This week, we’re pleased to profile the NCI-Nature Pathway Interaction Database (PID) in our weekly Spotlight series. Thanks to Kira Anthony from the PID for taking the time to talk with us, and for registering the PID BioGPS plugin.
The NCI-Nature Pathway Interaction Database (PID) contains open access curated and reviewed human cell signaling and regulatory pathways.
Why is your database unique and special?
The primary aspect that we feel distinguishes our pathways is their professional curation coupled with their review by experts in the field. Our pathways are composed of cellular processes and the biomolecular interaction types that are relevant to cell signaling such as binding, post-translational modification, transcription and translocation. We annotate each interaction with primary literature reference(s) and – to provide researchers with an indication of the type(s) of experimental support used to derive the physiologically relevant interaction – with evidence-type tag(s) called evidence code(s). The molecules found in a PID interaction can be proteins, complexes, compounds, and RNA. Each molecule is annotated with at least one external identifier such as for UniProt and Entrez Gene, and, where required for signaling, with an activity state, subcellular location, and post-translational modification(s).
We also provide users with the ability to perform a range of functions to facilitate pathway exploration. They can browse the list of pathways or search for their gene or protein of interest – all searches link to additional information such as network maps and detailed molecule pages, which themselves contain links to UniProt, Entrez Gene and the Gene Ontology. The PID batch query tool allows users to upload long lists(s) of molecules such as those obtained from microarray or proteomics experiments. These lists can either be overlaid onto predefined pathways or used to create a molecular connectivity map. Another powerful application of the database is the ability to create a novel network between any molecules of interest using the connected molecules tool. In addition, many researchers have expressed interest in obtaining the building blocks for pathways, so pathway reference lists and pathway molecule lists have recently been made available for download.
Finally, we feel it important to put the pathways curated by the NCI-Nature team in a broader cell signaling and bioinformatics context. To this end we have imported additional pathways from both BioCarta and Reactome. Coincident with our database updates we also include links to hot research articles in cell signaling with synopses written by the Nature Reviews team, and publish bioinformatics primers on other relevant online resources.
Who is your target audience?
The PID is aimed at the cancer research community and others interested in cellular pathways such as molecular cell biologists, immunologists, neuroscientists and developmental biologists. We continually populate the database with noteworthy pathways – as of September 2009, the database contains 96 pathways encompassing 5895 interactions. We believe that this abundance of information also provides bioinformaticians with the data necessary to perform large-scale analyses of signal transduction networks. The resources available for bioinformaticians and software developers include caGrid’s caBIO web services and APIs, along with database content available for download in XML and BioPAX Level 2 formats.
What improvements are coming in the future?
We are currently working hard to improve pathway visualization. Additionally, as some of our earlier pathways are now a couple of years old we are looking to make revisions that will take into account the significant recent advancements in certain fields. To suggest pathways for revision (or provide any other feedback), please drop us a line.
Thanks to the Kira and the PID team for registering their site as a BioGPS plugin, and for participating in our Spotlight series.