Representation of kidney structures in Uberon
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Presentation for KPMP Ontology Workshop Seattle July 2018
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Representation of kidney structures in Uberon
- 1. Representation of kidney structures in Uberon Chris Mungall cjmungall@lbl.gov KPMP Ontology Workshop Seattle July 2018
- 2. Uberon: multi- species anatomy ontology and knowledge graph Mungall et al. (2012). Genome Biology, 13(1), R5. doi:10.1186/gb-2012-13-1-r5 Köhler et al. (2014) F1000Research 2:30 Haendel et al. (2014) JBMS 5:21 doi:10.1186/2041-1480-5-21 http://uberon.org
- 3. CURIE: UBERON:0001230 PURL: http://purl.obolibrary.org/obo/UBERON_0001230 Label: glomerular capsule Synonyms: Bowman’s capsule, … Definition: A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus Xrefs: FMA:15626, EMAPA:28257, KUPO:0001001, ...
- 4. CURIE: UBERON:0001230 PURL: http://purl.obolibrary.org/obo/UBERON_0001230 Label: glomerular capsule Synonyms: Bowman’s capsule, … Definition: A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus Xrefs: FMA:15626, EMAPA:28257, KUPO:0001001, ... CURIE: UBERON:0004199 Label: S-shaped body RO:0002202 develops from CURIE: UBERON:0005750 Label: glomerular parietal epithelium BFO:0000050 part of CURIE: UBERON:0000487 Label: simple squamous epithelium CURIE: UBERON:0001286 Label: Bowman’s space subClassOf RO:0002220 adjacent to
- 5. CURIE: UBERON:0001230 PURL: http://purl.obolibrary.org/obo/UBERON_0001230 Label: glomerular capsule Synonyms: Bowman’s capsule, … Definition: A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus Xrefs: FMA:15626, EMAPA:28257, KUPO:0001001, ... CURIE: UBERON:0004199 Label: S-shaped body RO:0002202 develops from CURIE: GO:0003094 Label: glomerular filtration RO:0002215 capable of CURIE: UBERON:0005750 Label: glomerular parietal epithelium BFO:0000050 part of CURIE: UBERON:0000487 Label: simple squamous epithelium CURIE: UBERON:0001286 Label: Bowman’s space subClassOf RO:0002220 adjacent to CURIE: CL:1000452 Label: parietal epithelial cell
- 6. CURIE: UBERON:0000081 Label: metanephros CURIE: UBERON:0000080 Label: mesonephros CURIE: UBERON:0002120 Label: pronephros RO:0002202 develops from RO:0002202 develops from CURIE: UBERON:0002113 Label: kidney Uberon
- 7. CURIE: UBERON:0000081 Label: metanephros CURIE: UBERON:0000080 Label: mesonephros CURIE: UBERON:0002120 Label: pronephros RO:0002202 develops from RO:0002202 develops from EMAPA:17373EMAPA:27644EMAPA:16579 ZFA:0000151 ZFA:0000529 “kidney” CURIE: UBERON:0002113 Label: kidney Uberon EMAPA (mouse) ZFA (zebrafish)
- 8. Cross-species equivalence axioms • Mouse: – MA (adult) – EMAP (embryo, staged) – EMAPA (embryo, abstract) • Other models – XAO - Xenopus – ZFA – zebrafish – FBbt – Drosophila – WBbt – C elegans – DDAnat – Dictyostelium – … • Human – FMA (adult) – EHDAA2 (CS1-CS20) – SNOMED-CT – NIF GrossAnatomy (mammal brain) • Atlases – Allen (Brain) • Mouse (adult, embryo) • Human (adult, embryo) • Non-human Primate http://uberon.github.io/downloads.html#bridge
- 9. CURIE: UBERON:0002581 Label: postcentral gyrus CURIE: HBA:4085 Label: postcentral gyrus http://atlas.brain- map.org/atlas?atlas=265297125&structure=12899&rw=t#atlas=265297125&structure=4086&rw=t&resolution=202.08&x=36229.90171 3709674&y=36742.085905997985&zoom=-7&plate=112360981
- 10. Current uses of Uberon • Data annotation and discovery analytics – Expression and genomics data • http://bgeedb.org • FANTOM5, ENCODE – Integrating cross-species phenotype annotation • http://monarchinitiative.org/ – GO annotation • http://geneontology.org/ – Evo-devo – Others: FaceBase, HCA, … • Structuring of other ontologies – GO, CL, Phenotype ontologies, Disease ontologies, environment ontologies, … http://uberon.github.io/about/adopters.html
- 14. API access - biolink https://api.monarchinitiative.org/api/
- 15. Renal structure representation in Uberon Kidney Nervous system Whole organism Uberon classes 320 2,847 13,786 Cell types (CL) 134 688 2,199 Xrefs 1,097 16,706 51,247 Synonyms 830 11,422 37,794 Relationships 869 6,830 30,666 - Renal structures represent a relatively small fraction of overall information in Uberon - Brain and other nervous system structures represent a much higher fraction Changes made on request! https://github.com/obophenotype/uberon/issues
- 16. end
- 18. Role in KPMP • Metadata annotation • Discovery and analysis • Atlas integration
- 20. Uberon coordination with GO Alam-Faruque, Y., et al (2014). Representing Kidney Development Using the Gene Ontology. PloS One, 9(6), e99864. http://doi.org/10.1371/journal.pone.0099864
- 22. Uberon links with CL • Bidirectional links – What is this cell part of? • All ‘glomerular visceral epithelial cell’s are part of a glomerular capsule – What is this thing made of? • All ‘juxtaglomerular apparatus’ has part some ‘extraglomerular mesangial cell’ and has_part some ‘kidney granular cell’
- 23. Open Biological Ontologies (OBO) http://obofoundry.org 1. Well-integrated Modular ontologies 2. Provide technical and sociotechnological framework for cooperation 4. Enable feedback from community 3. Provide tools, best practices and infrastructure for forging new ontologies @obofoundry
- 24. sup por ts sup por ts supports supports supports supports supports supports supports supports supports supports supports supports supports supports supports supports supports supports sup por ts sup por ts sup por ts sup por ts Part of the OBO ontology landscape - modular coupling - building block approach {
- 25. supports
- 27. brain skull located in forebrain midbrain jaw hippocampus CA1 CA2 CNS neuron dopaminergic neuron Part Part Part Part Part Part Part Part Is-a cell Is-a
- 28. Anatomical data annotation phenotype 1 drug 2 brain skull located in forebrain midbrain jaw hippocampus CA1 CA2 CNS neuron dopaminergic neuron Part Part Part Part Part Part Part Part Is-a document 3gene 4 cell Is-a
- 29. Uses of anatomical ontologies • Transcriptome data – Genes expressed in hippocampal CA1 region • Describing clinical phenotypes – Loss of beta cells in the pancreas • Biospecimen annotation – Liver-derived sample • Functional characterization of gene products – BMP4 involved in bone development • Describing species diversity – Extant avians lack teeth but have feathers • NLP and text processing
- 30. Use cases for logical axioms • Use of is-a (Sub Class Of) – Tell me about phenotypes that affect bone growth • Answers include femur growth phenotypes • Use of part-of – Which genes are expressed in the hippocampus • Answers include genes expressed in CA1 region
- 31. Use of relationships in anatomical ontologies • Use of develops-from – Cancers of neural-crest lineage cells? • Answers include melanocytomas • Use of other relationship types – Structures are made from connective tissue? – Branches of the trigeminal nerve? – Brain regions associated with ataxia? – Neurons that secrete dopamine? – Brain regions near the striatum?
- 32. Ontologies built for one species will not work for others http://en.wikipedia.org/wiki/Pharyngeal_jaw
Editor's Notes
- Takehome: 1000 flowers blooming is ok but sometimes we need to garden TODO: change 4
- Takehome: Like software, reuse modular components TODO: pyramid; lego blocks
- Takehome: HPO is built in a modular fashion. Many benefits
- Takehome: HPO is built in a modular fashion. Many benefits