BICH 489-500 - CACAO

BICH 489-500 - CACAO

Biocurator Training Session

Plan for tonight

1. Pre-assessment survey2. Syllabus3. Review4. Annotation synthesis5. Practice!

Mutualistic Relationship

• We want you to get experience with: 1. CRITICALLY reading scientific papers 2. Bioinformatics resources3. Collaborating with other biocurators4. Synthesizing functional annotations

• We want to get high quality functional annotations to contribute back to the GO Consortium and other biological databases

Growing need for functional annotations

• Advances in DNA sequencing mean lots of new genomes & metagenomes

Growing need for high quality functional annotations

• High quality annotations allow us to infer the function of genes

• Which allows us to understand the capabilities of genomes and understand the patterns of gene expression

Classic MODel

Literature

Datasets

Curators(rate limiting)

Database

What does a functional annotation have to do with this course?

• Process of attaching information from the scientific literature to proteins

• CACAO will teach you to become a biocurator– you will be adding functional annotations to the biological database GONUTS

(http://gowiki.tamu.edu)

How is CACAO scored?• Points for a complete annotation

• GO term (right level of specificity)• Reference (paper)• Evidence code• Identify where in the paper the evidence is

• Refinements used to steal points for incorrect &/or incomplete annotations

• Identify a problem • Suggest correct alternative

• Refinements can be entered by any team (including the original team)

How can you get the annotations required by Rubric #2?

1. Synthesize complete & correct annotations.

2. Correctly refine (challenge & correct) someone else’s annotation.

3. If your annotation gets challenged, offer the best correction.

Functional annotation with Gene Ontology

• Controlled vocabulary with – Term identifiers

• GO:0000075– Name

• cell cycle checkpoint– Definitions

• "A point in the eukaryotic cell cycle where progress through the cycle can be halted until conditions are suitable for the cell to proceed to the next stage." [GOC:mah, ISBN:0815316194]

– Relationships• is_a GO:0000074 ! regulation of progression

through cell cycle

• Terms arranged in a Directed Acyclic Graph (DAG)

Why use Ontologies?

• Standardization• facilitate comparison across systems• facilitate computer based reasoning systems

– Good for data mining!

• leading functional annotation ontology = Gene Ontology (GO)

What is GO? Who is the GO Consortium (GOC)?

• GO = ~30,000 terms for gene product attributes

1. Molecular Function (enzyme activity)2. Biological Process (pathways)3. Cellular Component (parts of the cell)

• GO Consortium - set of biological databases that are involved in developing GO and contributing GO annotations

Cellular Component

• where a gene product acts

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

glucose-6-phosphate isomerase activityfigure from GO consortium presentations

Biological Process• a commonly recognized series of events

cell divisionFigure from Nature Reviews Microbiology 6, 28-40 (January 2008)

Which subontology (MF, BP or CC) would the following terms fit in?

GO:0001070 RNA binding transcription factor activity GO:0003677 DNA bindingGO:0009254 Peptidoglycan turnoverGO:0003918 DNA topoisomerase (ATP-hydrolyzing) activityGO:0006835 dicarboxylic acid transportGO:0009360 DNA polymerase III complexGO:0005694 ChromosomeGO:0008270 Zinc ion bindingGO:0000901 translation repressor activity, non-nucleic acid

binding

Part 1: Using GONUTS

Where can we find GO terms?

http://gowiki.tamu.edu

GONUTS

http://gowiki.tamu.edu/

Search for GO terms on GONUTShttp://gowiki.tamu.edu

• CHICK - AgBase (Gallus gallus)• dictyBase - dictyBase (Dictyostelium discoideum - slime mold)• FB - FlyBase (Drosophila melanogaster)• HUMAN - Reactome, BHF-UCL• MGI - Mouse genome informatics (Mus musculus - house mouse)• SGD - Saccharomyces genome database (Saccharomyces cerevisiase - yeast)• TAIR - The Arabidopsis Informatics Resource (Arabidopsis thaliana)• WB - WormBase (Caenorhabditis elegans)• ZFIN - Zebrafish model organism database (Danio rerio)

What do you actually need once you have found the correct term?

GO:0004713

Practice

1. What is the GO term for GO:0004713?2. What is the GO identifier for mitosis?3. How many results (ballpark) do you get when you search for cell division

using the Go, Search or G buttons?4. How many child terms are there for plasma membrane? How many

grandchildren?5. What term is the parent of GO:0006825?


What does a GO annotation consist of?

4 REQUIRED parts of EVERY GO annotation

GO

http://gowiki.tamu.edu/wiki/index.php/SGD:ADA2

** I will cover this again!!

4 Required Parts of a GO annotation (cont)

Evidence code

4 Required Parts of a GO annotation (cont)

Reference Notes (about evidence)

2 other parts that may be required…

Qualifier

With/from

Where are we adding GO annotations?


GONUTS

http://gowiki.tamu.edu/

…

Where do you add an annotation? Add a row in the table.

What you must fill in (for every annotation)

GO:0004713

PMID:1111IDA: Inferred from direct assay

Figure 2a

What you might also have to fill in

Not sure? Check the competition guidelines. Ask a coach (Jim, Debby, Adrienne or usually me)!

Questions?

1. You will be making functional (GO) annotations using GO terms.

2. You can search for GO terms on GONUTS.3. You will be adding your GO annotations to GONUTS.4. There are 4 required parts & 2 parts that may be

required in a GO annotation.5. You have to base your annotation on an experiment

published in a scientific paper.

What do we know so far?

Part 2: Finding proteins to annotate

What can you annotate?

• Proteins. – Any protein with a record in UniProt (Universal Protein Resource - http://uniprot.org)

• How can you find proteins to annotate?– Think of ways to identify a protein or paper to annotate

http://uniprot.org/

• Think• Consult your neighbor(s)

Choosing a protein to annotate

1. randomly2. topics of interest (ie efflux pump proteins, biofilms, marine biology)3. papers you have come across while doing other stuff4. methods you know or want to learn5. phenotypes and mutants you are interested in6. by author7. by pathway or regulon 8. suggested by another

- high ratio of IEA:manual annotations in GONUTS- mentioned in another class

9. current paper mentions another gene product10. review papers (ie Annual Reviews are excellent sources)11. Uniprot, GONUTS, WikiPathways, PubMed searches12. protein annotated by other teams13. ask a coach

Finding a scientific paper on a certain protein

• Has to be a scientific paper with experimental data in it.– Anything else is a valid reason to challenge!

• PubMed, PubMed Central, GoogleScholar…• No review articles• no books, textbooks, wikipedia articles, class notes…• You will need the PMID number

Practice - searching PubMed

1. How many papers do you get when you search for “coli”?2. How many of those papers are reviews?3. What is the title of the oldest paper when you search for “coli AND RNA

polymerase”?4. How many results are there when you search for “GTPase activity and

Gene Ontology”?5. What is the PMID of the paper when you search for “Hu JC AND coli AND

lysR AND 2010”?

http://pubmed.org

Why do we annotate on GONUTS?

• UniProt (Universal Protein Resource) will not let us annotate protein records on their site.

• They are a professionally-curated & closed database.

• GONUTS will.• GONUTS pulls the info from the UniProt record when it

makes a page for you to edit.

• UniProt - http://www.uniprot.org

Making a protein page on GONUTS requires a UniProt accession

http://www.uniprot.org/

Practice - Searching UniProt

Find the UniProt accessions for:a) Mouse Lsr proteinb) Diptheria toxin from Corynebacteriumc) mutS from E. coli K-12

http://uniprot.org

How do you make a new gene page in GONUTS?

1 2

• Use a UniProt accession to make a page on GONUTS that you can add your own annotations to.

• GoPageMaker will:- Check if the page exists in GONUTS & take you there if it does.- Make a page & pull all of the annotations from UniProt into a table that you can edit.

Practice

1. How many annotations are on the page for the p53 protein from humans?

2. How many different evidence codes are there on the page for the Bub1a protein from mice?

3. Give one of the paper identifiers for an annotation for the LpxK protein from E. coli.


Questions?

1. You will be making functional (GO) annotations using GO terms.2. You can search for GO terms on GONUTS.3. You will be adding your GO annotations to GONUTS.4. There are 4 required parts to a GO annotation.5. You have to base your annotation on an experiment published in a

scientific paper.6. You can annotate any protein with a record in

UniProt.7. You have to make a page in GONUTS for your

protein using the UniProt accession.


What are evidence codes?

• Describe the type of work or analysis done by the authors

• 5 general categories of evidence codes:1. Experimental2. Computational3. Author Statement4. Curator Assigned5. Automatically assigned by GO

• Describe the type of work or analysis done by the authors• 5 general categories of evidence codes:

1. Experimental2. Computational3. Author Statement4. Curator Assigned5. Automatically assigned by GO

• CACAO biocurators may only use certain experimental and computational evidence codes

What are the evidence codes?

Experimental Evidence Codes

• IDA: Inferred from Direct Assay• IMP: Inferred from Mutant Phenotype• IGI: Inferred from Genetic Interaction• IEP: Inferred from Expression Pattern• IPI: Inferred from Physical Interaction• EXP: Inferred from Experiment

Experimental Evidence Codes

• IDA: Inferred from Direct Assay• IMP: Inferred from Mutant Phenotype• IGI: Inferred from Genetic Interaction• IEP: Inferred from Expression Pattern• IPI: Inferred from Physical Interaction• EXP: Inferred from Experiment

http://geneontology.org/GO.evidence.shtml

Computational Evidence Codes

• ISS: Inferred from Sequence or Structural Similarity• ISO: Inferred from Sequence Orthology• ISA: Inferred from Sequence Alignment• ISM: Inferred from Sequence Model• IGC: Inferred from Genomic Context• IBA: Inferred from Biological Aspect of Ancestor• IBD: Inferred from Biological Aspect of Descendant• IKR: Inferred from Key Residues• IRD: Inferred from Rapid Divergence• RCA: Inferred from Reviewed Computational Analysis


Summary of Evidence Codes for CACAO

• IDA: Inferred from Direct Assay• IMP: Inferred from Mutant Phenotype• IGI: Inferred from Genetic Interaction• IEP: Inferred from Expression Pattern• 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 8, your annotation is incorrect!!!

Questions?

1. You will be making functional (GO) annotations using GO terms.2. You can search for GO terms on GONUTS.3. You will be adding your GO annotations to GONUTS.4. There are 4 required parts to a GO annotation.5. You have to base your annotation on an experiment published in a

scientific paper.6. You can annotate any protein with a record in

UniProt.7. You have to make a page in GONUTS for your

protein using the UniProt accession.


Practice - Identify the problem annotation(s) & why

1. GO:0003674 PMID:20372022 IDA: Inferred from Direct Assay Table 2. 2. GO:0016985 PMID:20372022 IMP: Inferred from Mutant Phenotype Table 2. 3. GO:0016985 PMID:20372022 IDA: Inferred from Direct Assay 4. GO:0016985 PMID:20372022 IDA: Inferred from Direct Assay Table 2. 5. GO:0003674 PMID:20372022 IDA: Inferred from Direct Assay Table 2.6. GO:0016985 PMID:20372002 IGI: Inferred from Genetic Interaction Table 2.7. GO:0016985 20372022 IDA: Inferred from Direct Assay Table 2.8. GO:0016985 PMID:20372002 EXP: Inferred from Experiment Table 2.

9. What is the UniProt accession of the protein described/annotated?

GO ID Reference Evidence Code Notes

Part 3: PRACTICE!Break!

Hypothetical Example #1 - Starting from a paper

• HYPOTHETICALLY, we have a paper (PMID:100) – the authors purify p53 protein from humans by

expressing a clone of the gene in E. coli.– They test for tyrosine kinase activity & report the

specific activity in Table 2.

Hypothetical Example #1 (cont)

• What is a suitable GO term?

• What is the UniProt accession of this protein?

• How do you make the page for this protein on GONUTS?

• How do you add your GO annotation?

Real Paper #2 - starting from a topic

• Topic: phenylalanine and phenylacetate catabolism in bacteria

Practice Paper #3

• http://www.ncbi.nlm.nih.gov/pubmed/3335830– Sequence Analysis of cDNA coding for a major house dust

mite allergen, Der p 1

1. CAN WE USE THIS PAPER?2. WHAT EVIDENCE CODE?

– A protein data-base search revealed that the Der p 1 amino acid sequence showed homology with a group of cysteine proteases. As shown in the composite alignment of the amino acid sequence Der p 1 and four cysteine proteases (Fig . 3), significant homology was observed in the amino and COOH-terminal regions of the proteins.

http://www.ncbi.nlm.nih.gov/pubmed/3335830

Summary

• You will be searching literature for experimental evidence for a protein’s function (MF), processes (BP) and location (CC)

Where do annotations show up?

Required parts (for every annotation)

GO:0004713

PMID:1111IDA: Inferred from direct assay

Figure 2a

What you might also have to fill in


BICH 489-500 - CACAO

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