PomBase December 2014: Difference between revisions
Line 55: | Line 55: | ||
Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V. Canto: An online tool for community literature curation. Bioinformatics. 2014 | 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. | 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 | b. Presentations including Talks and Tutorials and Teaching | ||
Line 107: | Line 108: | ||
University College London (Antonia Lock, for Ruth Lovering) | University College London (Antonia Lock, for Ruth Lovering) | ||
Oct Talk/Demo | Oct | ||
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 Curation Workshop | Nov | ||
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) | ||
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) | ||
Line 124: | Line 125: | ||
2013 | 2013 | ||
April | April | ||
ii) A configurable tool for community literature curation | 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 | June 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 | 2014 |
Revision as of 08:30, 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)
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