CACAO Training Fall 2012

Community Assessment of Community Annotation with Ontologies (CACAO)

Annotation Annotation: a note that is made while reading any form of text For scientists, 1.Nucleotide level: Where the genes are in the genome 2.Protein level: What their functions are From Wikipedia

Functional Annotation Annotation: a note that is made while reading any form of text Functional Annotation: a note in a specific format that is made based on evidence in a peer-reviewed paper about the attributes of a protein

Who classically makes functional annotations? Literature Datasets Biocurators (rate limiting) Database

What can you annotate? Proteins. PubMed for papers on a specific topic or protein or GO term Search UniProt for something interesting (i.e. allergen) or a protein of interest (i.e. PcnB) Check the references in the paper you are currently reading No matter what, you will need to find the protein’s accession on UniProt ( Use that accession to make a page for that protein on GONUTS ( Add your GO annotations to the protein’s page on GONUTS

How do you make a new protein page in GONUTS? GoPageMaker will:  Check if the page exists in GONUTS & take you there if it does.  Make a page if it does not exist in GONUTS already & pull all of the annotations from UniProt into a table that you can edit. Make as many protein pages as you would like. Do this first in case the paper has already been used to make GO annotations.

Practice – find a protein on UniProt (uniprot.org) Make a page for it on GONUTS (gowiki.tamu.edu) –ARE YOU LOGGED IN?! Once you’ve made the page, click on “edit Table” Scroll down & “add row” Cancel, cancel to get out of TableEditor

4 REQUIRED parts of EVERY GO annotation GO Evidence code Reference Notes (about evidence)

2 other parts that may rarely be required… With/From Qualifier

Where can you search for GO terms? GONUTS (gowiki.tamu.edu)

How do you know what GO term to search for or use? How do the authors describe the attributes of the protein? Is there a key word (i.e. check the title of the paper) you can search GONUTS for? After you make the page for the protein, is there a suitable term already used in an annotation in the Annotation table? (*** Also make sure your paper hasn’t already been annotated***) Stuck? Ask for help.

GO (Gene Ontology) Annotations 3 aspects (ontologies) for describing protein attributes: 1. Biological Process 2. Molecular Function 3. Cellular Component Controlled vocabulary –Everyone uses the same terms –Terms have 7 digit IDs that computers can understand Relationships between terms GO:

Molecular Function activities or “jobs” of a gene product GO: hexokinase activity From PMID: , rndsystems.com GO: Kinase activity

Biological Process a commonly recognized series of events GO: cell division From ridge.icu.ac.jp, edtech.clas.pdx.edu, scielosp.org GO: transcription, DNA dependent GO: pathogenesis

Cellular Component where a gene product acts From visualphotos.com, epmm.group.shef.ac.uk, GO: mitochondrion GO: peptidoglycan-based cell wall GO: ribosome

4 REQUIRED parts of EVERY GO annotation GO Evidence code Reference Notes (about evidence)

Summary of Evidence Codes for CACAO Evidence codes describe the type of work or analysis done by the authors IDA: Inferred from Direct Assay IMP: Inferred from Mutant Phenotype IGI: Inferred from Genetic Interaction ISO: Inferred from Sequence Orthology ISA: Inferred from Sequence Alignment ISM: Inferred from Sequence Model IGC: Inferred from Genomic Context If it’s not one of these 7, your annotation is incorrect!!!

2 other parts that may rarely be required… With/From Qualifier IGI: Inferred from Genetic Interaction ISO: Inferred from Sequence Orthology ISA: Inferred from Sequence Alignment ISM: Inferred from Sequence Model

Team & Individual Pages challenge

Challenges 1.Enter the reason for your challenge here. - (i.e. What’s wrong) 2. Provide the fix(es) for it.

UniProt – –Find your protein(s) here (UniProt accession required) PubMed – –Find your papers about the protein’s attributes (molecular function, biological process, cellular component) GONUTS – –Search for GO terms –Make page for your protein on GONUTS (using UniProt accession) –Add your annotation to the protein’s Annotation table during first (Annotation) week of any round –Review and challenge competitors’ annotations during the second (challenge) week of any round

CACAO I Go to UniProt & look for more interesting proteins What is your favorite microorganism? What topics are in interested in? What proteins have you heard about in classes? Make pages for them on GONUTS Look for papers about the proteins on PubMed Has to have experimental data in it! Look for a suitable GO term What terms are already in the Annotations table? If not, try searching based on a keyword in the paper Add an annotation

CACAO II We will collectively decide on some challenges & we will assess other GO annotations BOMMO:Q3LFR2

What to look for: 1.Is the annotation on the right protein’s page? (Is the paper about the protein?) 2.Is the annotation complete? Does it have the 4 required parts? Does the annotation require either of the additional 2 fields (i.e. does the annotation use an evidence code that needs the with/from field filled in)? 3.Has the student used information NOT allowed by the CACAO rules (i.e. evidence code or binding terms)? 4.Do the notes point to a figure/table that supports the annotation? (i.e. no review articles, no model figures, no crystal structures, etc) 5.Is there a more suitable GO term (more or less specific)? 6.Does the evidence code fit with the experiment described? 7.For IGI, ISO, or ISA have they entered the correct accession in the with/from field? 8.For ISO & ISA, does the protein in the with/from field have a GO annotation that has experimental evidence for that GO term? (i.e. Does the annotation maintain a direct chain of evidence?) 9.Is the annotation complete, correct and accurate based on the paper? (i.e. will it be submitted to UniProt?)