Thursday, July 9, 2015

See you at ISMB-ECCB 2015!

The 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2015) hosted by the International Society for Computational Biology (ISCB) will be held together with the 14th Annual European Conference on Computational Biology (ECCB 2015), jointly as ISMB/ECCB 2015. This year the conference is being held in lovely Dublin and a bunch of us from UniProt will be in attendance!

We will be presenting talks and posters at the Special Interest Groups being held before the conference and also at the main conference itself. UniProt's PI, Alex Bateman, will also be co-chairing the conference this year! Would you like to hear about the latest developments in UniProt and interesting new projects that we've been working on? Do you have some questions about UniProt that you'd like to discuss? Or maybe you'd just like to see some friendly faces in Dublin while you're there? Come find one of us! Below is a list of who are, where we'll be and what we'll be presenting. Tweet us or message us on facebook. We're looking forward to seeing you there!

Saturday, 11 July 2015
09.40 to 10.00
Claire O’Donovan - Building a community for genome and proteome annotation
Talk in the AFP (Automated Function Prediction) SIG
11.10 to 11.30
Tunca Dogan - UniGOPred and ECPred : Automated Function Prediction Tools Based on A Combination of Different Classifiers
Talk in the AFP (Automated Function Prediction) SIG
15.05 to 16.10
Tunca Dogan - Protein Function Prediction in UniProt with the Comparison of Structural Domain Arrangements
Poster in the AFP (Automated Function Prediction) SIG
Sunday, 12 July 2015
17.45 to 19.00
Andrew Nightingale - Bringing protein functional positional annotation knowledge into reference genomes
Poster (odd) A37
17.45 to 19.00
Tunca Dogan - ECPred: Enzyme Prediction Using a Combination of Classifiers
Poster (odd) L63
Monday, 13 July 2014
14.00 to 14.20
Benoit Bely - The Universal Protein Resource (UniProt): New Development on Proteomes, Variation and Proteomics
Tech Track talk
17.45 to 19.00
Michele Magrane - Recent developments in UniProt: improving access to protein knowledge
Poster (even) P2
17.45 to 19.00
Tunca Dogan - Computational drug target prediction and validation in PI3K/AKT pathway
Poster (even) A18
17.45 to 19.00
Rabie Saidi - Association Rule Mining for Metabolic Pathway Prediction
Poster (even) L04
17.45 to 19.00
Maria Martin - Improving protein knowledge by Integrating proteomics data with UniProt Reference protein sets
Poster (even) M12

Wednesday, July 1, 2015

Do you have a protein to share with the world?

Did you know that you can submit protein sequences directly to UniProt to be included in our database? We accept protein sequences that have been determined at protein level (via Edman degradation or manual interpretation of tandem-mass spectrometry data) and have clear species identification.

The UniProt home page contains a link in the 'UniProt data' section' that says 'Submit your data'. This takes you to a UniProt help page about data submission.. Just follow the link for submitting protein sequences to get started! Submission is done using SPIN, a web-based tool where you can enter your protein sequence and any associated biological information. All of the information required to create a database entry will be collected during the submission process.

You can submit large batches of multiple sequences as well as individual sequences. A UniProt curator will then review your submission and create a reviewed (UniProtKB/Swiss-Prot) entry for each submitted sequence. Once your protein is inUniProtKB, it will be assigned a stable accession number which can be used in publications. Data can be kept confidential until publication.

Note that translations of coding sequences (CDS) submitted to the EMBL-Bank/GenBank/DDBJ nucleotide sequence resources are automatically transferred to the TrEMBL section of UniProtKB and do not need to be submitted to UniProtKB separately:

The direct submissions we get often include interesting proteins like toxins or anti-freeze proteins and sometimes even proteins from extinct organisms! For example, here's a fragment of a Neanderthal bone protein that we received as a direct submission

So if you would like to make your sequences accessible to other researchers, even if they are fragments, just send them in with their species and identification method. If you have any questions, please feel free to write to us at