PomBase December 2014: Difference between revisions
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b. Presentations including Talks and Tutorials and Teaching | b. Presentations including Talks and Tutorials and Teaching | ||
April 2013 | |||
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 2013 | ||
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 2013 | ||
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 2013 | ||
Curation Workshop: Title: Genome Annotation | Curation Workshop: Title: Genome Annotation | ||
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Cambridge University Part II Systems Biology (Valerie Wood) | Cambridge University Part II Systems Biology (Valerie Wood) | ||
Dec | Dec 2013 | ||
Lecture and Practical: Title: An introduction to Data analysis and curation using PomBase | Lecture and Practical: Title: An introduction to Data analysis and curation using PomBase | ||
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April | April 2014 | ||
Demonstration/ presentation: 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 | ||
July | July 2014 | ||
Lecture and Workshop: Title: Using PomBase: Exploring Fission Yeast Data Online | Lecture and Workshop: Title: Using PomBase: Exploring Fission Yeast Data Online | ||
EMBO course “Molecular genetics with fission yeast”, Institut Pasteur, Paris (Midori Harris) | EMBO course “Molecular genetics with fission yeast”, Institut Pasteur, Paris (Midori Harris) | ||
May | May 2014 | ||
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) | ||
Oct | Oct 2014 | ||
Talk/Demo: Title: Canto Curation Tool | Talk/Demo: Title: Canto Curation Tool | ||
WormBase Scientific Advisory Board, Hinxton Hall, Cambridge (Valerie Wood) | WormBase Scientific Advisory Board, Hinxton Hall, Cambridge (Valerie Wood) | ||
Nov | Nov 2014 | ||
Curation Workshop: Title: Genome Annotation | Curation Workshop: Title: Genome Annotation | ||
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c. Poster presentations | c. Poster presentations | ||
April | April 2013 | ||
Biocurator 2013, Cambridge, UK | Biocurator 2013, Cambridge, UK | ||
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* ii) A configurable tool for community literature curation | * ii) A configurable tool for community literature curation | ||
June EMBO Conference on Fission Yeast: Pombe 2013, UCL, London, UK | June 2013 | ||
EMBO Conference on Fission Yeast: Pombe 2013, UCL, London, UK | |||
* i) A configurable tool for community literature curation | * i) A configurable tool for community literature curation | ||
* ii) PomBase.org | * ii) PomBase.org | ||
* iii) Using Gene Ontology biological process co-annotation for ontology and annotation quality control | * iii) Using Gene Ontology biological process co-annotation for ontology and annotation quality control | ||
2014 | April 2014 | ||
British Yeast Group, Exeter, U.K. 2014 | |||
* i) PomBase, the scientific resource for fission yeast | * i) PomBase, the scientific resource for fission yeast | ||
Biocurator 2014, Toronto, Canada | |||
* i) Using Gene Ontology biological process co-annotation for ontology and annotation quality control | * i) Using Gene Ontology biological process co-annotation for ontology and annotation quality control | ||
* ii) PomBase: The Model Organism Database for fission yeast | * ii) PomBase: The Model Organism Database for fission yeast |
Revision as of 08:44, 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
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
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. (GO used for analysis)
b. Presentations including Talks and Tutorials and Teaching
April 2013
Workshop: Title: Gene Ontology Annotation Workshop University College London (Antonia Lock, for Ruth Lovering)
Aug 2013
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 2013
Lecture: Title: Biological Databases: Data Types and Connections Computational Biology MPhil students, University of Cambridge (Midori Harris)
Nov 2013
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 2013
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)
April 2014
Demonstration/ presentation: Title: Canto: A tool for ontology based curation by expert curators and the scientific community Community curation workshop, Biocurator 2014, Toronto
July 2014
Lecture and Workshop: Title: Using PomBase: Exploring Fission Yeast Data Online EMBO course “Molecular genetics with fission yeast”, Institut Pasteur, Paris (Midori Harris)
May 2014
Workshop: Title: Gene Ontology Annotation Workshop University College London (Antonia Lock, for Ruth Lovering)
Oct 2014
Talk/Demo: Title: Canto Curation Tool WormBase Scientific Advisory Board, Hinxton Hall, Cambridge (Valerie Wood)
Nov 2014
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)
c. Poster presentations
April 2013
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 2013
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
April 2014
British Yeast Group, Exeter, U.K. 2014
- i) PomBase, the scientific resource for fission yeast
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
Ontology Development Contributions
Cell Cycle Overhaul
Co-organized the Cell Cycle ontology meeting at Hinxton (Feb 2013). This overhaul generated 181 Source Forge tickets, of which 30 are still open. Continuing effort:
* i) Developing curation guidelines for cell cycle annotation * ii) Reannotation to more specific terms based on revised ontology and annotation guidelines * iii) Writing up Cell cycle report for publication
General Ontology Development
Most new terms required by PomBase are now requested via TermGenie templates, or TermGenie free form. Many other types of ontology issues (missing parent, true path violations, term merge requests, etc.) are reported on the GO SourceForge tracker (~200 tickets in 2013–2014, 115 still open)
Annotation Quality control (Annotation intersections)
PomBase has developed many in-house QC procedures for GO annotation. We are slowly documenting these and making them more widely available. QC using BP co-annotations have been presented in posters, and on GO annotation calls. The first rules have been generated for inclusion in GO Jenkins checks, and have been used to correct annotation errors in UniProt and most MODs. These “annotation intersection” checks have also resulted in the correction of many incorrect mappings from InterPro and Uniprot (IEA) reported here https://sourceforge.net/p/geneontology/annotation-issues/milestone/InterPro/ https://sourceforge.net/p/geneontology/annotation-issues/milestone/GOA/
PomBase Display of annotation extensions : New Feature
PomBase compact GO view : New Feature
- PomBase curators participate in Annotation conference calls