ICAR2016 TAIR talk

TAIR: A Sustainable Community Resource for Arabidopsis Research

International Conference on Arabidopsis Research (ICAR 2016), GyeongJu, Korea

1.  TAIR: a sustainable community resource for Arabidopsis research (Eva Huala)

2.  Using biological ontologies to accelerate progress in plant biology research (Donghui Li)

3.  Community annotation: making your data and publication more discoverable (Donghui Li)

Using biological ontologies to accelerate progress in plant biology research

Donghui Li

TAIR/Phoenix Bioinformatics

Every year, an average of: •  Over 3000 Arabidopsis research articles are added •  Over 2000 papers are associated with genes •  Over 400 articles have gene function, expression or

phenotype data extracted •  Over 5000 experiment-based annotations are added

using controlled vocabularies (GO and PO ontologies)

Producing a ‘gold standard’ annotated reference plant genome

Highly structured, searchable, computable functional annotations

•  How do we use biological ontologies to annotate Arabidopsis gene function?

•  How to read/interpret annotations?

•  What can you do with these annotations?

Outline

Why do we need ontologies?

Inconsistency in free text: Different names for the same concept

translation, protein synthesis Same name for different concepts

Bud initiation?

A Gene Ontology (GO) term

Accession: GO:0006412 Name: translation Ontology: biological_process Synonyms: protein anabolism, protein biosynthesis, protein biosynthetic process, protein formation, protein synthesis, protein translation Definition: The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. Source: GOC:go_curators

molecular function: catalytic / binding activities kinase activity, DNA binding activity

biological process: biological goal or objective

protein translation, mitosis cellular component: location or complex

nucleus, ribosome, proteasome

More info at www.geneontology.org

Gene Ontology (GO)

Terms in an ontology are connected

is_a

part_of

Annotation at different depth of the ontology

is_a

part_of

Retrieval at higher nodes in the ontology

is_a

part_of

Manual literature annotation

Gene product GO term

Evidence code

Anatomy of a GO annotation

Reference

Experimental evidence codes (EXP) IDA Inferred from Direct Assay (enzyme assays, in situ hybridization) IMP Inferred from Mutant Phenotype (analysis of visible trait) IPI Inferred from Physical Interaction (yeast-2-hybrid) IEP Inferred from Expression Pattern (RT-PCR, Western blot) IGI Inferred from Genetic Interaction (double mutant analysis)

Examples

http://geneontology.org/page/guide-go-evidence-codes

Commonly used evidence codes

Experimental evidence codes (EXP) IDA Inferred from Direct Assay (enzyme assays, in situ hybridization) IMP Inferred from Mutant Phenotype (analysis of visible trait) IPI Inferred from Physical Interaction (yeast-2-hybrid) IEP Inferred from Expression Pattern (RT-PCR, Western blot) IGI Inferred from Genetic Interaction (double mutant analysis) Computational Analysis Evidence Codes (non-EXP) ISS Inferred from Sequence or Structural Similarity

- based on published sequence alignment IEA Inferred from Electronic Annotation

- InterPro2GO

Examples

http://geneontology.org/page/guide-go-evidence-codes

Commonly used evidence codes

Evidence code

Annotation counts %

Evidence code

Annotation counts %

EXP 95,435 34.7 IDA 56,271 20.4 IEP 6,651 2.4 IGI 4,286 1.6 IMP 19,441 7.1 IPI 8,786 3.2

Non-EXP 179,801 66.2 Total 275,236 101

Summary of Arabidopsis GO annotations in TAIR

Notes: 9,186 unique publications used in EXP annotations Based on TAIR ATH_GO_GOSLIM.txt 2016-06-05

Based on annotation data as of May 24, 2016

Summary of Arabidopsis GO annotations in TAIR

-  Querygenefunc,oninforma,on-  GOannota,onprojec,on-  Func,onalcategoriza,on-  Termenrichment

Application: What can you do with TAIR GO/PO annotations?

Get annotations for individual genes from the TAIR locus page

Gene Ontology annotations

Plant Ontology annotations

Get annotations for individual genes from the TAIR locus page

Other functional information:

Gene summary Polymorphism

Phenotype Publications

Gene symbols

Get annotations for a list of genes



Find genes annotated to a GO/PO term

Download all GO/PO annotations



Source: http://geneontology.org/page/current-go-statistics 2016-06-03

Rat

Human

Mouse

Arabidopsis Zebrafish

Worm Chicken

Fly Yeast Rice E coli

GO annotations by species

Annotating new plant genomes by projecting GO terms from Arabidopsis onto other non-model plant species based on gene orthology

EnsemblPlants Compara

•  Use the Compara pipeline to build orthology •  Automatically transfer GO annotations to plant orthologs

Rulesü  atleasta40%pep,deiden,tytoeachotherü  onlyGOannota,onswithanevidencetypeofIDA,IEP,IGI,

IMPorIPIareprojectedü  noannota,onswitha'NOT'qualifierareprojectedü  annota,onstotheGO:0005515proteinbindingtermarenot

projected



TAIR’s functional categorization tool

Cellular component

Molecular function

Biological process

Biological process

Functional category Gene count

Overrepresentation statistical test:

In my list of genes, are any functional classes (for example a GO process) found more often than

expected when compared with the reference list?

Term enrichment analysis

GOC provides a term enrichment tool powered by PANTHER

pantherdb.org geneontology.org

Input 1

Input 2

ID Mapping

Use up-to-date annotations

Output 168/26684=0.63% 0.63%x442=2.78

Model for the regulation of long-term drought responses in Q. suber root

Model for ABA-dependent drought response in cork oak

1  The main activity of TAIR curators is producing a ‘gold standard’

annotated reference genome dataset by integrating experimental data from the research literature. New annotations are constantly added.

2  One common use of TAIR is to infer the function of genes in agriculturally important species based on orthology to Arabidopsis genes.

3  TAIR’s annotations are used in applications such as functional categorization, term enrichment. It is important to use the latest annotation file from TAIR.

Summary

Community annotation: making your data and publication more discoverable

Donghui Li

Community annotation on TAIR

Why should everyone participate - increased exposure of your work

Community annotation on TAIR

1. Pre-publication: register your gene symbol to minimize accidental duplications in gene nomenclature

2. Preparing your manuscript: include AGI locus identifiers

3. Post-publication: submit your annotation to us (any journal)

Tips to make your research more discoverable

AT1G56650 PAP1 PRODUCTION OF ANTHOCYANIN PIGMENT 1AT2G01180 PAP1 PHOSPHATIDIC ACID PHOSPHATASE 1AT2G27190 PAP1 PURPLE ACID PHOSPHATASE 1AT3G16500 PAP1 PHYTOCHROME-ASSOCIATED PROTEIN 1

Gene name duplication make it harder to find the right gene

Plant Cell Physiol. 2010 Jun;51(6):866-76

Plant Cell Physiol. Jun;51(6):877-83

Conflicting nomenclature / error in publication not uncommon

PMID:21447788

Mandatory requirement for publishing in some journals

Always include AGI codes

How to submit

Requires a login so we can credit submitter no subscription required

Video tutorial

Provide ‘evidence with’ as comments

Multiple genes?

•  “I do profit a lot from the data on TAIR, thus

this submission is a small contribution to extend the data present on TAIR.”

•  “I gratefully did it [data submission] because I already benefit from similar information for other genes.”

Community feedback

Q&A

ICAR2016 TAIR talk

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