CACAO TrainingFall 2012

Community Assessment ofCommunity 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 (http://uniprot.org)

Use that accession to make a page for that protein on GONUTS (http://gowiki.tamu.edu)

Add your GO annotations to the protein’s page on GONUTS

How do you make a new protein page in GONUTS?

1

2

• 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.

Annotations

edit table

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

GOEvidence

code

ReferenceNotes (about evidence)

2 other parts that may rarely be required…

With/From

Qualifier

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

- http://gowiki.tamu.edu- http://www.ebi.ac.uk/QuickGO- http://amigo.geneontology.org

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 Process2. Molecular Function3. Cellular Component

• Controlled vocabulary– Everyone uses the same terms– Terms have 7 digit IDs that computers can

understand

• Relationships between terms

GO:0005886

Molecular Function• activities or “jobs” of a gene product

GO:0004396 hexokinase activity

From PMID:9341134, rndsystems.com

GO:0016301 Kinase activity

Biological Process• a commonly recognized series of events

GO:0051301 cell division

From ridge.icu.ac.jp, edtech.clas.pdx.edu, scielosp.org

GO:0006351 transcription, DNA dependent

GO:0009405 pathogenesis

Cellular Component• where a gene product acts

From visualphotos.com, epmm.group.shef.ac.uk, http://www.cellsignal.com/products/2415.html

GO:0005739 mitochondrion

GO:0009274 peptidoglycan-based

cell wall

GO:0005840 ribosome

4 REQUIRED parts of EVERY GO annotation

GOEvidence

code

ReferenceNotes (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!!!

http://gowiki.tamu.edu/wiki/index.php/evidence_codes

2 other parts that may rarely be required…

With/From

Qualifier

IGI: Inferred from Genetic InteractionISO: Inferred from Sequence OrthologyISA: Inferred from Sequence AlignmentISM: 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 – http://uniprot.org– Find your protein(s) here (UniProt accession required)

• PubMed – http://pubmed.org– Find your papers about the protein’s attributes (molecular function,

biological process, cellular component)

• GONUTS – http://gowiki.tamu.edu– 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

http://gowiki.tamu.edu/wiki/index.php/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?)