1. CACAO Training
ASM-JGI 2012

2. Transferring information to new genomes
Database
Lists of genes
Known functions of
Homologs or subsets
New knowledge
This figure describes an ideal situation for how we obtain/transfer information to new genes/genomes
How well in works depends on the quantity and quality of what we can get out of the databases.
The problem is…

3. Curation is rate limiting
Literature
Database
Biocurators
(rate limiting)
Datasets

4. CACAO is growing

5. CACAO biodiversity
Spring 2012
Annotations

6. CACAO 2
CACAO changes the job of the professionals from primary curation to assessment
Growth in CACAO makes assessment rate limiting
Solution: Promote CACAO veterans to help with assessment

7. BIOCURATORS

8. The biocurator training …

9. What’s in it for you? We hope you will
learn how we think about protein function
gain skills that will help your future career
enjoy contributing to a resource used by people all over the world
have fun!

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

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

12. 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

13. Functional Annotation
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
Specific format = GO (Gene Ontology) Annotation

14. 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:

15. GO:0004347 hexokinase activity
Molecular Function
activities or “jobs” of a gene product
GO: hexokinase activity
GO: Kinase activity
From PMID: , rndsystems.com

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

17. GO:0009274 peptidoglycan-based cell wall
Cellular Component
where a gene product acts
GO terms: mitochondrion, mitochondrial membrane, mitochondrial matrix, mitochondrial intermembrane space
GO: peptidoglycan-based cell wall
GO: ribosome
GO: mitochondrion
From visualphotos.com, epmm.group.shef.ac.uk,

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

23. What do you actually need once you have found the correct term?
GO:

24. Functional Annotation
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
Specific format = GO (Gene Ontology) Annotation
Peer-reviewed paper

25. Finding a scientific paper
Has to be a scientific paper with experimental data in it. (Anything else is a valid reason to challenge!!)
No review articles, no books, no textbooks, no wikipedia articles, no class notes…
You will need the PMID number
Inspiration ok, not suitable for reference section
Biocurators can annotate the same paper as previous semesters, but they have to synthesize NOVEL annotations (can’t just remake the same annotations = no points!)

26. Functional Annotation
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
Specific format = GO (Gene Ontology) Annotation
Peer-reviewed paper
Protein

27. 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
Can either show this list after they have run out of suggestions or write them in as the students suggest them.

28. Why do you need an accession from UniProt (http://www.uniprot.org)?
* UniProt is not accessible for us to annotate protein on, so we use a community-contributed website, GONUTS. GONUTS needs the UniProt accession so it can pull the existing annotations from UniProt into GONUTS.
However, correct and complete annotations are being submitted to the GO Consortium and then get added to UniProt (as part of the GO Consortium) *
UniProt is not editable by the community, but GONUTS is.
GONUTS can make a page that has the annotations from UniProt for any protein using it’s UniProt accession.
Correct & complete annotations at the end of the competition will be submitted back to UniProt.

29. How do you make a new protein page in GONUTS?2 1
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!

30. Annotations
edit table

31. Functional Annotation
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
Specific format = GO (Gene Ontology) Annotation
Peer-reviewed paper
Protein

32. Annotations
edit table

33. Form for your annotation (when you edit the table)

34. 4 REQUIRED parts of EVERY GO annotation
Reference GO
Notes (about evidence)
Evidence
code
There are 24 rows in the annotations table on this protein’s page. Each row is a separate annotation. Suzi added the ones with the white background.
The annotation shown on the slide is from a different protein’s page. It is merely to show what an annotation is.

35. 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!!!

36. Functional Annotation
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
Specific format = GO (Gene Ontology) Annotation
Peer-reviewed paper
Protein
Evidence code

37. 4 REQUIRED parts of EVERY GO annotation
Reference GO
Notes (about evidence)
Evidence
code
There are 24 rows in the annotations table on this protein’s page. Each row is a separate annotation. Suzi added the ones with the white background.
The annotation shown on the slide is from a different protein’s page. It is merely to show what an annotation is.

38. 2 other parts that may rarely be required…
Qualifier
With/From

39. How is CACAO scored? Rounds
Points for a complete AND correct annotation (normally 1 week/round, today = 25 mins)
4 necessary parts
May be additional parts
NOTE: We will take away points if the annotation is not correct when assessed by an experienced CACAO biocurator
Challenges are used to steal points for incorrect &/or incomplete annotations (normally 1 week/round, today = 20 mins)
Identify a problem
Suggest correct alternative
Refinements can be entered by any team (during any challenge week)
Important part: challenges. These are what make the difference every semester in the final standings!!!
also: My rubrics require min 15 correct annotations for 4 rounds of CACAO for excellent grade for Rubric #2
3 ways to get those:
Complete & Correct annotations
Refine & correct someone else’s annotation
Refine an annotation of yours that was refined by another team but not corrected completely.

40. Scoreboard & Challenges

41. Team & Individual Pages
challenge

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

43. Annotation discussion (aka argument)

44. UniProt – http://uniprot.org PubMed – http://pubmed.org
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

45. ASM-JGI Competition! You now have 25 mins to:
Use the assigned paper for your group and …
Find the correct UniProt accession
Make the page for the protein on GONUTS
Make at least one annotation
You will have 20 mins to challenge other teams’ annotations
What fields are wrong & why?!