PomBase December 2015: Difference between revisions
(Progress report) |
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=== 2. Annotation progress === | === 2. Annotation progress === | ||
==== 2.a Annotation Breadth ==== | |||
{| class="wikitable" cellpadding="5" | {| class="wikitable" cellpadding="5" | ||
!Annotation Type !! l| | !Annotation Type !! l| Nov 2014 !! Nov 24, 2015 | ||
|- | |- | ||
| Total Number of Genes: 2014 | | Total Number of Genes: (2014 * protein coding only) || 5052* || 5451 | ||
|- | |- | ||
|Total Genes with at least one (non root) GO || | |Total Genes with at least one (non root) GO || 5279 || 5289 | ||
|- | |- | ||
|Total Genes with at least one (non root) BP || 4316* || 4668 | |Total Genes with at least one (non root) BP || 4316* || 4668 | ||
|- | |- | ||
|Total Genes with at least one (non root) CC || 4894* || 5191 | |Total Genes with at least one (non root) CC || 4894* || 5191 | ||
|- | |- | ||
|Total Genes with at least one (non root) MF || 3682* || 3958 | |Total Genes with at least one (non root) MF || 3682* || 3958 | ||
|- | |- | ||
| Total Annotations: || 39233 || 40718 | | Total Annotations: || 39233 || 40718 | ||
|- | |- | ||
|colspan= | |colspan=3 align=center bgcolor=white| '''Annotation by Experiment''' | ||
|- | |- | ||
|Total genes | |Total genes with experimental annotation ||4572||4558 | ||
|- | |- | ||
|Total | |Total annotations by experiment ||18568 ||20912 | ||
|- | |- | ||
|colspan= | |colspan=3 align=center bgcolor=white| '''Annotation by Orthology''' | ||
|- | |- | ||
|Total Genes Annotated by Orthology || | |Total Genes Annotated by Orthology ||3196|| 3484 | ||
|- | |- | ||
|Total | |Total Annotations by orthology ||9624 || 9346 | ||
|- | |- | ||
| Annotation by PomBase|| | | Annotation by PomBase||8994|| 9134 | ||
|- | |- | ||
| Annotation by GOA-UniProt || | | Annotation by GOA-UniProt ||119|| 128 | ||
|- | |- | ||
| Annotation by GOC || | | Annotation by GOC ||468 || 4 | ||
|- | |- | ||
|colspan= | |colspan=3 align=center bgcolor=white| '''IEA Annotation''' | ||
|- | |- | ||
|Total Annotations: ||5342 || 4290 | |Total Annotations: ||5342 || 4290 | ||
|} | |} | ||
==== 2.b Annotation Depth ==== | |||
We ensure annotation depth is maintained by identifying terms where it should always be possible to make a more specific annotation. | |||
The current list of restricted terms is 1220, with only 56 violations (all annotation sources). | |||
==== 2.c Annotation extensions ==== | |||
4223 extensions on 799 gene products | |||
=== 3. Methods and strategies for annotation === | === 3. Methods and strategies for annotation === | ||
Line 67: | Line 76: | ||
C. Priorities for annotation: | C. Priorities for annotation: | ||
i. Literature describing the characterization of previously unknown genes, or genes previously unstudied in fission yeast | * i. Literature describing the characterization of previously unknown genes, or genes previously unstudied in fission yeast | ||
ii. Approval of community curation submissions (new publications) | * ii. Approval of community curation submissions (new publications) | ||
iii. Legacy papers related to well studied processes, especially those providing 'direct substrate' annotation extension to build high quality networks/pathways based on GO data see "regulation of mitotic cell cycle" http://tinyurl.com/osp4nnq | * iii. Legacy papers related to well studied processes, especially those providing 'direct substrate' annotation extension to build high quality | ||
networks/pathways based on GO data see "regulation of mitotic cell cycle" http://tinyurl.com/osp4nnq | |||
Priority processes | Priority processes | ||
* | * mitotic chromosome segregation (including spindle checkpoint) (vw) | ||
* G2/M and metaphase/anaphase cell cycle transitions (vw) | * G2/M and metaphase/anaphase cell cycle transitions (vw) | ||
* cytokinesis (vw) | * cytokinesis (vw) | ||
Line 79: | Line 89: | ||
(There are no genes with no GO annotation, or only IEA/ISO but with available literature as these are processed immediately) | (There are no genes with no GO annotation, or only IEA/ISO but with available literature as these are processed immediately) | ||
=== 4. Presentations and publications === | === 4. Presentations and publications === | ||
==== a. Papers with substantial GO content ==== | |||
* An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System. Hoffman CS, Wood V, Fantes PA. | |||
Genetics. 2015 Oct;201(2):403-23. doi: 10.1534/genetics.115.181503. PMID: 26447128 | |||
* PomBase 2015: updates to the fission yeast database. McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V. Nucleic Acids Res. 2015 Jan;43(Database issue):D656-61. doi: 10.1093/nar/gku1040. Epub 2014 Oct 31. PMID: 25361970 | |||
b. Presentations including Talks and Tutorials and Teaching | ==== b. Presentations including Talks and Tutorials and Teaching ==== | ||
pombe2015 - Eighth International Fission Yeast Meetin Kobe, Japan, 21-26 June 2015 | |||
* How to get more from PomBase - a brief tour of PomBase gene pages, curated data types, querying, tools, and external links (VW) | |||
* Community curation using Canto - how to create, edit and submit annotations based on published experiments (MAH) | |||
* Hidden in plain sight: The eukaryotically conserved unstudied proteins and a framework for their classification and characterisation | |||
Cambridge University, teaching | |||
c. Poster presentations with GO content | * Curation Workshop: Title: Genome Annotation Cambridge University Part III Biochemistry (VW, MAH, AL) | ||
* Lecture: Title: Databases and Genome Annotation (Semantic Systems Biology) Cambridge University Part II Systems Biology (VW) | |||
==== c. Poster presentations with GO content ==== | |||
pombe2015 - Eighth International Fission Yeast Meetin Kobe, Japan, 21-26 June 2015 | |||
* Hidden in plain sight: The eukaryotically conserved unstudied proteins and a framework for their classification and characterisation | |||
27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB), Levico Terme, Italy, 6-12 September 2015 | |||
* Hidden in plain sight: The eukaryotically conserved unstudied proteins and a framework for their classification and characterisation | |||
=== 5. Other Highlights === | === 5. Other Highlights === | ||
'''A. GO terms and related contributions by PomBase''' | '''A. GO terms and related contributions by PomBase''' | ||
Line 97: | Line 132: | ||
http://tinyurl.com/qzz7kn9 | http://tinyurl.com/qzz7kn9 | ||
Requested | Requested 185 new terms via term Genie | ||
Submitted 960 electronic mapping update requests | Submitted 960 electronic mapping update requests | ||
Line 105: | Line 140: | ||
'''B. Annotation outreach and user advocacy efforts''' | '''B. Annotation outreach and user advocacy efforts''' | ||
See workshops and presentation above | See workshops and presentation above. | ||
We answer many GO related queries via our helpdesk and this is reflected in the large number of PomBase FAQ items referring to GO http://www.pombase.org/faq | |||
Solicited 78 responses to GO servey via PomBase 'collector' | |||
'''C. Other highlights''' | '''C. Other highlights''' | ||
1. | 1. We have piloted a system to generate high quality physical networks directly from Gene Ontology annotation data. We are currently using these networks to target literature curation gaps. | ||
Dataset | Dataset | ||
http://www.pombase.org/documentation/high-confidence-physical-interaction-network | http://www.pombase.org/documentation/high-confidence-physical-interaction-network | ||
Line 130: | Line 169: | ||
4. Developing curation rules to improve curation depth and accuracy | 4. Developing curation rules to improve curation depth and accuracy | ||
http://www.slideshare.net/ValerieWood/pombase-internal-rules-for-curation-using-ontologies | http://www.slideshare.net/ValerieWood/pombase-internal-rules-for-curation-using-ontologies | ||
Includes | Includes: | ||
* Removing IEA redundancy PomBase filters >87% of available IEA annotation (covered by manual annotation). Redundant experimental annotations are not filtered. | |||
* Flagging high level GO terms as "not for direct annotation". PomBase excludes 1120 GO terms for direct annotation. | |||
5. We have developed Canto, an intuitive web-based interface to support literature curation using ontologies, and a literature management environment. Canto supports GO curation and is a generic component of the GMOD project and can be easily configured for use with other organisms, and ontologies. Currently Canto is being extended to fully support annotation extensions by community curators by restricting curator options based on domain and range of terms applicable to a given relationship. We are also working to use taxon constraints to limit available term choices by species. | 5. We have developed Canto, an intuitive web-based interface to support literature curation using ontologies, and a literature management environment. Canto supports GO curation and is a generic component of the GMOD project and can be easily configured for use with other organisms, and ontologies. Currently Canto is being extended to fully support annotation extensions by community curators by restricting curator options based on domain and range of terms applicable to a given relationship. We are also working to use taxon constraints to limit available term choices by species. | ||
6. Community curation. Over 300 papers fully or partially curated by the fission yeast community (includes GO, and other data types: phenotypes, modifications, genetic and physical interactions) | |||
7. Our phenotype ontology FYPO now has over 4000 terms with logical definitions that refer to GO terms (using over 900 different GO terms) |
Latest revision as of 05:47, 26 November 2015
PomBase, December 2015
PomBase is the Model Organism Database for the fission yeast Schizosaccharomyces pombe (www.pombase.org)
1. Staff working on GOC tasks
PomBase GO curators: Valerie Wood, Midori Harris, Antonia Lock
Developers associated with GO related projects at PomBase: online curation tool, pipelines, Website, automated QC, Query tools: Mark McDowall, Kim Rutherford
NO STAFF FUNDED BY GO OR GOC GRANTS
2. Annotation progress
==== 2.a Annotation Breadth ====
Annotation Type | Nov 2014 | Nov 24, 2015 |
---|---|---|
Total Number of Genes: (2014 * protein coding only) | 5052* | 5451 |
Total Genes with at least one (non root) GO | 5279 | 5289 |
Total Genes with at least one (non root) BP | 4316* | 4668 |
Total Genes with at least one (non root) CC | 4894* | 5191 |
Total Genes with at least one (non root) MF | 3682* | 3958 |
Total Annotations: | 39233 | 40718 |
Annotation by Experiment | ||
Total genes with experimental annotation | 4572 | 4558 |
Total annotations by experiment | 18568 | 20912 |
Annotation by Orthology | ||
Total Genes Annotated by Orthology | 3196 | 3484 |
Total Annotations by orthology | 9624 | 9346 |
Annotation by PomBase | 8994 | 9134 |
Annotation by GOA-UniProt | 119 | 128 |
Annotation by GOC | 468 | 4 |
IEA Annotation | ||
Total Annotations: | 5342 | 4290 |
2.b Annotation Depth
We ensure annotation depth is maintained by identifying terms where it should always be possible to make a more specific annotation. The current list of restricted terms is 1220, with only 56 violations (all annotation sources).
2.c Annotation extensions
4223 extensions on 799 gene products
3. Methods and strategies for annotation
A. Literature curation:
PomBase curation focus is on literature curation. PomBase does not have dedicated GO curators but curate all aspects of papers including GO, phenotypes (single and multi gene, alleles names and descriptions, conditions), modifications, modifiers, upstream, downstream targets, genetic and physical interactions, complementations, orthology, disease associations, proteins features, gene co-ordinates, other sequence features)
Community curation
B. Computational annotation strategies:
C. Priorities for annotation:
- i. Literature describing the characterization of previously unknown genes, or genes previously unstudied in fission yeast
- ii. Approval of community curation submissions (new publications)
- iii. Legacy papers related to well studied processes, especially those providing 'direct substrate' annotation extension to build high quality
networks/pathways based on GO data see "regulation of mitotic cell cycle" http://tinyurl.com/osp4nnq
Priority processes * mitotic chromosome segregation (including spindle checkpoint) (vw) * G2/M and metaphase/anaphase cell cycle transitions (vw) * cytokinesis (vw) * DNA metabolism (mah) * signalling pathways (al) * conjugation (al)
(There are no genes with no GO annotation, or only IEA/ISO but with available literature as these are processed immediately)
4. Presentations and publications
a. Papers with substantial GO content
- An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System. Hoffman CS, Wood V, Fantes PA.
Genetics. 2015 Oct;201(2):403-23. doi: 10.1534/genetics.115.181503. PMID: 26447128
- PomBase 2015: updates to the fission yeast database. McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V. Nucleic Acids Res. 2015 Jan;43(Database issue):D656-61. doi: 10.1093/nar/gku1040. Epub 2014 Oct 31. PMID: 25361970
b. Presentations including Talks and Tutorials and Teaching
pombe2015 - Eighth International Fission Yeast Meetin Kobe, Japan, 21-26 June 2015
- How to get more from PomBase - a brief tour of PomBase gene pages, curated data types, querying, tools, and external links (VW)
- Community curation using Canto - how to create, edit and submit annotations based on published experiments (MAH)
- Hidden in plain sight: The eukaryotically conserved unstudied proteins and a framework for their classification and characterisation
Cambridge University, teaching
- Curation Workshop: Title: Genome Annotation Cambridge University Part III Biochemistry (VW, MAH, AL)
- Lecture: Title: Databases and Genome Annotation (Semantic Systems Biology) Cambridge University Part II Systems Biology (VW)
c. Poster presentations with GO content
pombe2015 - Eighth International Fission Yeast Meetin Kobe, Japan, 21-26 June 2015
- Hidden in plain sight: The eukaryotically conserved unstudied proteins and a framework for their classification and characterisation
27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB), Levico Terme, Italy, 6-12 September 2015
- Hidden in plain sight: The eukaryotically conserved unstudied proteins and a framework for their classification and characterisation
5. Other Highlights
A. GO terms and related contributions by PomBase
Submitted 2228 term or ontology update requests http://tinyurl.com/qzz7kn9
Requested 185 new terms via term Genie
Submitted 960 electronic mapping update requests http://tinyurl.com/oh45ouh
B. Annotation outreach and user advocacy efforts
See workshops and presentation above.
We answer many GO related queries via our helpdesk and this is reflected in the large number of PomBase FAQ items referring to GO http://www.pombase.org/faq
Solicited 78 responses to GO servey via PomBase 'collector'
C. Other highlights
1. We have piloted a system to generate high quality physical networks directly from Gene Ontology annotation data. We are currently using these networks to target literature curation gaps. Dataset http://www.pombase.org/documentation/high-confidence-physical-interaction-network Access to process based high confidence interaction networks http://www.pombase.org/browse-curation/fission-yeast-go-slim-terms
2. Increasing GO slim breadth
http://www.pombase.org/browse-curation/fission-yeast-go-slim-terms
Proteins with a biological process annotation not covered by the slim (gene count: 115)
Proteins with no GO slim or biological process annotation (gene count: 756)
3. Creating inventories of conserved and non conserved unstudied genes
http://www.pombase.org/status/priority-unstudied-genes
In fission yeast the "unknown" inventory is around 831 entries, many of which are apparently species-specific. However, a large number (511) are conserved, and a significant number of these (183) have orthologs in vertebrates.
4. Developing curation rules to improve curation depth and accuracy
http://www.slideshare.net/ValerieWood/pombase-internal-rules-for-curation-using-ontologies
Includes:
- Removing IEA redundancy PomBase filters >87% of available IEA annotation (covered by manual annotation). Redundant experimental annotations are not filtered.
- Flagging high level GO terms as "not for direct annotation". PomBase excludes 1120 GO terms for direct annotation.
5. We have developed Canto, an intuitive web-based interface to support literature curation using ontologies, and a literature management environment. Canto supports GO curation and is a generic component of the GMOD project and can be easily configured for use with other organisms, and ontologies. Currently Canto is being extended to fully support annotation extensions by community curators by restricting curator options based on domain and range of terms applicable to a given relationship. We are also working to use taxon constraints to limit available term choices by species.
6. Community curation. Over 300 papers fully or partially curated by the fission yeast community (includes GO, and other data types: phenotypes, modifications, genetic and physical interactions)
7. Our phenotype ontology FYPO now has over 4000 terms with logical definitions that refer to GO terms (using over 900 different GO terms)