EMBL-EBI Annual Scientific Report 2012

InterProOur team co-ordinates the InterPro and Metagenomics projects atEMBL-EBI. InterPro integrates protein data from 11 major sources,classifying them into families and predicting the presence of domains andfunctionally important sites.InterPro has a number of important applications, including the automatic annotation of proteins for UniProtKB/TrEMBL andgenome annotation projects. InterPro is used by Ensembl and in the GOA project to provide large-scale mapping of proteins toGO terms.Metagenomics is the study of the sum of genetic material found in an environmental sample or host species, typically usingnext-generation sequencing (NGS) technology. The Metagenomics Portal, a resource established at EMBL-EBI in 2011,enables metagenomics researchers to submit sequence data and associated descriptive metadata to the public nucleotidearchives. Deposited data is subsequently functionally analysed using an InterPro-based pipeline, and the results generated arevisualised via a web interface.Major achievementsWe redesigned and re-launched the InterPro website inlate 2012, and played a key role in the EMBL-EBI websiteredesign process. We also built a new InterPro search facilitythat utilises the central EBI search engine. Search results arenow much easier to interpret and browse: the engine behavesin a Google-like manner, allowing users to enter wildcards(e.g., * and ?), use logic (AND or NOT), search with singlewords or phrases and quickly select subsets of the resultsusing faceted filtering. InterPro results are now paginated andhighlight the context of the query terms.The new EMBL-EBI website, which will launch in early 2013,features improved discoverability of InterPro and otherresources. Global EBI search results are shown in categorieson local search pages to encourage users to explore the datain different ways.In 2012 we moved the InterPro DAS and BioMart services tothe London Data Centres; the main InterPro website will jointhem there shortly.The InterPro database continues to benefit from improvedcoverage of UniProtKB proteins, increasing to 80.8% in thelatest release (v. 40.0). This is partly due to significant datacuration and integration efforts, which led to an additional2355 signatures being incorporated into the databasein 2012.Focussed curation of InterPro2GO term associations ledto 334 additional entries being assigned GO terms; 44%of entries now have at least one term associated. The totalnumber of GO mappings has increased by 838, despite aconcerted effort to remove terms that are too general (andtherefore uninformative) or erroneously mapped. In 2012 wepublished the first paper describing how this highly utilisedannotation resource is created and maintained.InterProScan5 is poised to take over as the main InterProscanning software in 2013. Multiple release candidates weremade publicly available in 2012, each containing new featuresand improved implementation.InterPro Scan 5:release candidate 4 features• Search all 11 member databases, plus four additionalalgorithms: Phobius, TMHMM, Coils and SignalPv4;• Predict potential membership of a protein in a pathwaybased on InterPro results;• Use a BerkeleyDB-based protein match look-up servicethat reduces calculation overheads by only searchingsequences not already found in UniProtKB (install thislocally or query the EBI-hosted service);34 2012 EMBL-EBI Annual Scientific Report