A merger of multi-species anatomy               ontologies                   orAn experiment in knowledge management      ...
We want to understand gene          function across taxa                                          Vertebrata              ...
Anatomy ontologies built for one               species will not work for others                                           ...
So we build species-specific ontologies                                                                                   ...
But this results in silos                                                                                                 ...
Why not just map ontology terms?Class A                 Class B                        Mapped?   Useful?FMA: extensor     ...
Avoiding Silo-izationUse ontologies that are:     open     documented     reusable     interoperable     built accord...
Long ago in the world of anatomies                                 CARO                                   FMA             ...
And then came Uberon, created to     bridge model organism anatomies                                 CARO                 ...
Subsumption of species-specific classes                      is_a (SubClassOf)                                           a...
Uberon                                           UBERON includes the                                      cerebellum      ...
Use of Uberon Annotation extensions GOA/UniProtKB [Chris’ talk] Construction of GO terms [Heikos talk] Bgee cross-model...
Fossils, the ultimate silo Modern diversity only a fraction ofevolutionary diversity Missing evolutionary transitions e....
And so over time…                                        CARO                                       UBERON                ...
But…                                        CARO                                       UBERON                             ...
And there was asynchrony in the           universe
The big roll-up                                   CARO                               UBERON-ext                           ...
The new Uberon-ext Contents:   – Over 8,000 classes (terms), 2500+ added by Phenoscape   – Multiple relationships, includ...
Example of ontology roll-up
Managing variation: using reasoners           to detect errors                                                    only_in_...
What can you do with the new               uberon-ext?                                              kb.phenoscape.org Rea...
Different strokes for different folksontology     contentsbasic        simple             relationshipshttp://purl.obolibr...
Conclusions Model organism anatomies were difficult to query   across Uberon was developed to help integrate human and  ...
Thanks!       Chris Mungall, JimBalhoff, Frederic Bastian, David   Blackburn, Aurelie Comte     , Wasila Dahdul , Alex Dec...
Looking for a post-doc?     http://nescent.org/about/employment.php#PostDoc2We are recruiting a postdoc with training in b...
Upcoming SlideShare
Loading in...5
×

A merger of multi-species anatomy ontologies

483

Published on

Biocuration presentation of Uberon anatomy ontology merge with TAO, VSAO, and AAO; and the history of anatomy ontologies.

0 Comments
2 Likes
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total Views
483
On Slideshare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
7
Comments
0
Likes
2
Embeds 0
No embeds

No notes for slide
  • Maybe update examples here
  • Pull out? Make more CL centric?
  • Fantom5? Anything else to put here?
  • Alex do you have a higher res image of the limbs?
  • Uberon uses the only_in_taxon method to make relationships such as lactifierous gland only in taxonMammalia and boneonly in taxon Vertebrata. These relations are useful for human users of the ontology, and can be used forconsistency checking within the ontology. For example if the FBbt class “tibia” (representing a segment ofan insect leg) were accidentally placed as a child of UBERON:0000979 tibia, this would be flagged by thereasoner because tibia is a bone, bones are found only in vertebrates, and FBbt is a Drosophila ontology
  • A merger of multi-species anatomy ontologies

    1. 1. A merger of multi-species anatomy ontologies orAn experiment in knowledge management Biocuration 2013 Chris Mungall, Jim Balhoff, Frederic Bastian, David Blackburn, Aurelie Comte , Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzi Lewis, Paula Mabee, Anne Niknejad, Melissa Haendel
    2. 2. We want to understand gene function across taxa Vertebrata tetrapod limbs Ascidians ampullae Echinodermata tube feet Arthropoda Annelida parapodia MolluscaAnatomy ontologies are used to describe morphological variation
    3. 3. Anatomy ontologies built for one species will not work for others http://ccm.ucdavis.edu/bcancercd/22/mouse_figure.htmlhttp://fme.biostr.washington.edu:8080/FME/index.html
    4. 4. So we build species-specific ontologies FMA is_a (SubClassOf) EHDAA2 part_of develops_from surrounded_by organ system solid organ pharyngeal region respiratory primordium respiratory parenchymatous lung bud system organ lung MA Lower thoracic respiratory lobular organ organ system tract cavity MPO abnormal respiratory thoracic respiratory system morphology system cavity organ pleural sac lung abnormal lung morphology lung abnormal pulmonary acinus morphology pulmonary acinus abnormal pulmonary lung alveolus morphology alveolar sac alveolus
    5. 5. But this results in silos FMA is_a (SubClassOf) EHDAA2 part_of develops_from surrounded_by organ system solid organ pharyngeal region respiratory primordium respiratory parenchymatous lung bud system organ lung MA Lower thoracic respiratory lobular organ organ system tract cavity MPO abnormal respiratory thoracic respiratory system morphology system cavity organ pleural sac lung abnormal lung morphology lungabnormal pulmonary acinus morphology pulmonary acinus abnormal pulmonary lung alveolus morphology alveolar sac alveolus
    6. 6. Why not just map ontology terms?Class A Class B Mapped? Useful?FMA: extensor MouseAnatomy: retina Yes Noretinaculum of wristVivo: legal decision Cognitive Atlas: decision Yes NoPlantOntology: Pith MouseAnatomy: medulla Yes NoTaxRank: domain NCI: protein domain Yes NoZfishAnat: hypophysis MouseAnatomy: pituitary No YesTAO:fossa AdverseReactions: depression Yes NoFMA: colon GAZ: Colón, Panama Yes NoQuality: male Chebi: maleate 2(-) Yes NoString matching for mapping can lead to spurious results andsemantics of mappings and provenance are not always clear
    7. 7. Avoiding Silo-izationUse ontologies that are:  open  documented  reusable  interoperable  built according to shared principles  reuse core relations and patternsProblem: How do we re-use in the presence of variability?
    8. 8. Long ago in the world of anatomies CARO FMA EMAP EHDAA2 MA (mostly) FBbt embryonic embryonic XAO ZFA Adult adultDrosophila mouse human Xenopus zebrafish mouse human An anatomical reference ontology was built to help standardize species-specific ontologies
    9. 9. And then came Uberon, created to bridge model organism anatomies CARO UBERON FMA EMAP EHDAA2 MA (mostly) FBbt embryonic embryonic XAO ZFA Adult adultDrosophila mouse human Xenopus zebrafish mouse human
    10. 10. Subsumption of species-specific classes is_a (SubClassOf) anatomical part_of structure develops_from capable_of is_a (taxon equivalent) endoderm only_in_taxon organ part foregut swim bladder organ endoderm of forgut NCBITaxon: respiration organ Actinopterygii respiratory primordium GO: respiratory gaseous exchange pulmonary acinus alveolus lung lung primordiumNCBITaxon: Mammalia alveolus of lung alveolar sac lung bud FMA: pulmonary FMA:lung MA:lung alveolus EHDAA: MA:lung alveolus lung bud Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., & Haendel, M. A. (2012). http://genomebiology.com/2012/13/1/R5
    11. 11. Uberon UBERON includes the cerebellum p pCell Ontology cerebellar cerebellum i to enable i vermis posterior lobequery across i i granularity cerebellum i i cerebellum p p p pposterior cerebellum cerebellar vermis of lobe of posterior vermis cereblleum cerebellum lobe MA:mouse p FMA:human p dendrite dendrite CL:Purkinje cell CL:Purkinje cell axon axon GO/NIF: subcellular GO/NIF: subcellular
    12. 12. Use of Uberon Annotation extensions GOA/UniProtKB [Chris’ talk] Construction of GO terms [Heikos talk] Bgee cross-model homology-based expression search [Frederic’s talk] Annotation of biospecimens from diverse taxa [eagle-i.org] Phenotype similarity analyses to identify disease gene candidates and models  New project “Monarch Initiative” to build tools and services for navigating phenotypes [see our poster tonight]  PhenoDigm analysis engine [Damian’s talk tomorrow]
    13. 13. Fossils, the ultimate silo Modern diversity only a fraction ofevolutionary diversity Missing evolutionary transitions e.g.fin to limb Extant ontologies not always Shubin et al. 2006compatible with fossil data Different data sources and resolutionbetween extinct and extant
    14. 14. And so over time… CARO UBERON vHOG Arthropod Vertebrate Homologous Organs Group HAO AAO TAOHymenoptera VSAO Amphibian Teleost Vertebrate Skeletal FMA EMAP EHDAA2 MA (mostly) FBbt embryonic embryonic XAO ZFA Adult adult Drosophila mouse human Xenopus zebrafish mouse human … additional multi-species ontologies evolved
    15. 15. But… CARO UBERON vHOG Arthropod Vertebrate Homologous Organs Group HAO AAO TAOHymenoptera VSAO Amphibian Teleost Vertebrate Skeletal FMA EMAP EHDAA2 MA (mostly) FBbt embryonic embryonic XAO ZFA Adult adult Drosophila mouse human Xenopus zebrafish mouse human …they had a hard time maintaining relationships to one another
    16. 16. And there was asynchrony in the universe
    17. 17. The big roll-up CARO UBERON-ext Uberon core CL Cell Ontology VSAO AAO TAO Vertebrate Skeletal Amphibian Teleost FMA EMAP EHDAA2 MA (mostly) embryonic embryonic XAO ZFAAdult adult mouse human Xenopus zebrafishmouse human
    18. 18. The new Uberon-ext Contents: – Over 8,000 classes (terms), 2500+ added by Phenoscape – Multiple relationships, including subclass, part-of and develops- from Scope: metazoa (animals) – Current focus is chordates – Includes teleost, amniote, and amphibian specific classes Uberon classes are generic / species neutral – ‘mammary gland’: you can use this class for any mammal! – ‘lung’: you can use this class for any vertebrate (that has lungs)http://purl.obolibrary.org/obo/uberon/ext.obohttp://purl.obolibrary.org/obo/uberon/ext.owl
    19. 19. Example of ontology roll-up
    20. 20. Managing variation: using reasoners to detect errors only_in_taxon UBERON: bone Vertebrata disjoint with is_a is_aDrosophila melanogaster UBERON: tibia Homo sapiens is_a is_a ✗ part_of part_of Fruit fly FBbt ‘tibia’ Human FMA ‘tibia’ Developmental Biology, Scott Gilbert, 6th ed.
    21. 21. What can you do with the new uberon-ext? kb.phenoscape.org Reason across anatomical variation in extinct and extant taxa Query for candidate genes relevant to morphological evolution Modified from Ahn and Ho 2008
    22. 22. Different strokes for different folksontology contentsbasic simple relationshipshttp://purl.obolibrary.org/obo/uberon/basic.owluberon main ontology http://purl.obolibrary.org/obo/uberon.owlmerged main ontology + links to GO, CL, NCBITaxon, NBOhttp://purl.obolibrary.org/obo/uberon/merged.owlComposite- Uberon plus species-specific ontology classes merged inmetazoan http://purl.obolibrary.org/obo/uberon/composite-metazoan.owlUberon-ext Uberon merged plus TAO, AAO and VSAO terms merged in http://purl.obolibrary.org/obo/uberon/ext.owl Formats:http://uberon.org OBO-Format OWL
    23. 23. Conclusions Model organism anatomies were difficult to query across Uberon was developed to help integrate human and model organism anatomy Uberon has been useful to align model organism anatomy ontologies Palaeontolosts and evo-devo biologists needed wider coverage A core set of vertebrate terms was needed by all=> So we merged the ontologies, and now we can havedinosaur bone data, model organism data, and humandata all integrated and queryable in one database!
    24. 24. Thanks! Chris Mungall, JimBalhoff, Frederic Bastian, David Blackburn, Aurelie Comte , Wasila Dahdul , Alex Dececchi, Nizar Ibrahim, Suzi Lewis, Paula Mabee, Anne Niknejad
    25. 25. Looking for a post-doc? http://nescent.org/about/employment.php#PostDoc2We are recruiting a postdoc with training in bioinformatics who is interested in studyingphenotypic evolution by combining model organism genetic data with comparativeanatomical data from throughout the vertebrates. Projects may range from primarilycomputational to primarily biological.
    1. A particular slide catching your eye?

      Clipping is a handy way to collect important slides you want to go back to later.

    ×