PomBase December 2014: Difference between revisions

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April
April
Workshop: Title: Gene Ontology Annotation Workshop
Workshop: Title: Gene Ontology Annotation Workshop
University College London (Antonia Lock, for Ruth Lovering)
University College London (Antonia Lock, for Ruth Lovering)


Aug
Aug
Talk: Title:  Fission Yeast as a Model for Systems Biology  (Covering GO, QC using annotation intersections, annotation extensions, and cell cycle ontology content meeting)
Talk: Title:  Fission Yeast as a Model for Systems Biology  (Covering GO, QC using annotation intersections, annotation extensions, and cell cycle ontology content meeting)
University of Trondheim, Norway  (Valerie Wood)
University of Trondheim, Norway  (Valerie Wood)


Oct
Oct
Lecture: Title: Biological Databases: Data Types and Connections
Lecture: Title: Biological Databases: Data Types and Connections
Computational Biology MPhil students, University of Cambridge (Midori Harris)
Computational Biology MPhil students, University of Cambridge (Midori Harris)


Nov
Nov
Curation Workshop: Title: Genome Annotation
Curation Workshop: Title: Genome Annotation
Cambridge University Part III Biochemistry (Valerie Wood,  Midori Harris, Antonia Lock)
Cambridge University Part III Biochemistry (Valerie Wood,  Midori Harris, Antonia Lock)


Nov Lecture  
Lecture: Title: Databases and Genome Annotation (Semantic Systems Biology)
Title: Databases and Genome Annotation (Semantic Systems Biology)
Cambridge University Part II Systems Biology  (Valerie Wood)
Cambridge University Part II Systems Biology  (Valerie Wood)


Dec Lecture and Practical  
Dec
Title: An introduction to Data analysis and curation using PomBase
 
Lecture and Practical: Title: An introduction to Data analysis and curation using PomBase
Wellcome Trust Fission Yeast Workshop, Hinxton, Cambridge  (Valerie Wood)
Wellcome Trust Fission Yeast Workshop, Hinxton, Cambridge  (Valerie Wood)


Dec Talk/ Demo  
Talk/ Demo: Title: Evaluating the functional annotation status of K. pastoris and implementing Canto for community curation
Title: Evaluating the functional annotation status of K. pastoris and implementing Canto for community curation
BIOLEDGE Consortium Meeting, Wolfson College, Cambridge  (Valerie Wood)
BIOLEDGE Consortium Meeting, Wolfson College, Cambridge  (Valerie Wood)


Line 91: Line 94:
2014
2014


April Demonstration/ presentation
April
Title: Canto: A tool for ontology based curation by expert curators and the scientific community
 
Demonstration/ presentation: Title: Canto: A tool for ontology based curation by expert curators and the scientific community
Community curation workshop, Biocurator 2014, Toronto
Community curation workshop, Biocurator 2014, Toronto

Revision as of 08:28, 11 December 2014

PomBase Summary, 2013/2014

Staff

Three PomBase curation staff (V. Wood, M Harris, A Lock) are working on GO-related tasks, none funded by the GO grant.

Annotation Progress

Of the 5052 protein coding genes, none-root node annotations are assigned for:

* GO:0003674 - molecular_function 3682/5052
* GO:0005575 - cellular_component 4894/5052
* GO:0008150 - biological_process 4316/5052
* Only 89 proteins have ND annotation for all 3 aspects

PomBase currently provide 39233 annotation in total. PomBase uses filtering to remove redundant IEA annotation from the GAF. If an IEA annotation is represented by an annotation with a manual evidence code, the IEA annotation is filtered reducing the number of IEAs from *** to 5342.

ncRNAs are fully annotated using available literature (other than rRNA, tRNA, snRNA and snoRNA, most have no functional information).

The fission yeast literature corpus comprises ~5000 curatable publications, of which 1808 have been fully curated.

Methods and strategies for annotation (please note % effort on literature curation vs. computational annotation methods)

a. Literature curation: > 95%

b. Computational annotation strategies: < 5% (for the 2911 currently unpublished gene products)

c. Priorities for annotation

At present, PomBase curators are mainly curating historical papers. All new papers are assigned to the authors for first pass curation (currently 234 publications have been community curated).

The highest priority is to capture annotations where new information is available for an Uncharacterized gene product. These papers are identified during the literature triage process.

We are moving towards process- and gene-based annotation for efficiency. Effort is currently focussed on cell cycle, cytokinesis, chromosome segregation, DNA metabolism, chromatin modification and sporulation. We hope to be able to refine annotations for the well-studied genes so that they can be used to automatically generate LEGO diagrams.

PomBase curators are routinely creating terms via the new TermGenie interface to speed up the process of annotation.

PomBase curators are capturing more specificity for annotations by adding substrate, targets etc in the Annotation Extension column (aka col-16) using the protein2GO interface. ADD NUMBERS

PomBase curators are up to date with the GAF checks on Jenkins and the protein2GO error checks

PomBase compact GO view : New Feature

Presentations and Publications

a. Papers with substantial GO content

McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V. PomBase 2015: updates to the fission yeast database. Nucleic Acids Res. 2014 Oct 31

Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG. Improving functional annotation for industrial microbes: a case study with Pichia pastoris. Trends Biotechnol. 2014 Aug;32(8):396-9.

Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014 May 21;15(1):155. Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V. Canto: An online tool for community literature curation. Bioinformatics. 2014 Hayles J, Wood V, Jeffery L, Hoe K-L, Kim D-U, Park H-O, Salas-Pino S, Heichinger C, Nurse P. A genome-wide resource of cell cycle and cell shape genes of fission yeast. Open Biol 2013 3: 130053.

b. Presentations including Talks and Tutorials and Teaching

2013

April

Workshop: Title: Gene Ontology Annotation Workshop University College London (Antonia Lock, for Ruth Lovering)

Aug

Talk: Title: Fission Yeast as a Model for Systems Biology (Covering GO, QC using annotation intersections, annotation extensions, and cell cycle ontology content meeting) University of Trondheim, Norway (Valerie Wood)

Oct

Lecture: Title: Biological Databases: Data Types and Connections Computational Biology MPhil students, University of Cambridge (Midori Harris)

Nov

Curation Workshop: Title: Genome Annotation Cambridge University Part III Biochemistry (Valerie Wood, Midori Harris, Antonia Lock)

Lecture: Title: Databases and Genome Annotation (Semantic Systems Biology) Cambridge University Part II Systems Biology (Valerie Wood)

Dec

Lecture and Practical: Title: An introduction to Data analysis and curation using PomBase Wellcome Trust Fission Yeast Workshop, Hinxton, Cambridge (Valerie Wood)

Talk/ Demo: Title: Evaluating the functional annotation status of K. pastoris and implementing Canto for community curation BIOLEDGE Consortium Meeting, Wolfson College, Cambridge (Valerie Wood)


2014

April

Demonstration/ presentation: Title: Canto: A tool for ontology based curation by expert curators and the scientific community Community curation workshop, Biocurator 2014, Toronto

July Lecture and Workshop Title: Using PomBase: Exploring Fission Yeast Data Online EMBO course “Molecular genetics with fission yeast”, Institut Pasteur, Paris (Midori Harris)

May Workshop Title: Gene Ontology Annotation Workshop University College London (Antonia Lock, for Ruth Lovering)

Oct Talk/Demo Title: Canto Curation Tool WormBase Scientific Advisory Board, Hinxton Hall, Cambridge (Valerie Wood)

Nov Curation Workshop Title: Genome Annotation Cambridge University Part III Biochemistry (Valerie Wood, Midori Harris, Antonia Lock)

Nov Lecture Title: Databases and Genome Annotation (Semantic Systems Biology) Cambridge University Part II Systems Biology (Valerie Wood)


c. Poster presentations

2013

April Biocurator 2013, Cambridge, UK i) Using biological process co-annotation for ontology and annotation quality control

ii) A configurable tool for community literature curation

June EMBO Conference on Fission Yeast: Pombe 2013, UCL, London, UK i) A configurable tool for community literature curation ii) PomBase.org iii) Using Gene Ontology biological process co-annotation for ontology and annotation quality control

2014


April British Yeast Group, Exeter, U.K. 2014 PomBase, the scientific resource for fission yeast

April Biocurator 2014, Toronto, Canada i) Using Gene Ontology biological process co-annotation for ontology and annotation quality control ii) PomBase: The Model Organism Database for fission yeast

Other Highlights

  • PomBase curators participate in Annotation conference calls