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Phenoscape Grant Renewal Workshop/Notes

Phenoscape II: Tuesday, April 28, 1:00-5:30

Participating: Phenoscape: Paula Mabee, Todd Vision, Monte Westerfield, Hilmar Lapp, Wasila Dahdul, Jim Balhoff, Cartik Kothari, Peter Midford, John Lundberg; Suzanna Lewis, Judy Blake, Peter Vize, Anne Maglia

• Will be extending the taxonomic scope to extant and extinct vertebrates
  • Create an annotation database spanning the taxonomic scope and their anatomy ontologies
  • Three multi-species anatomy ontologies are being developed: teleosts, amphibians, mammalian anatomy
  • Tree mapping: show when an evolutionary phenotype first appeared
• EQ support in all involved model organism databases
  • Structure of MP is not consistent with anatomy, or with PATO
  • Mapping from MP to EQ syntax is being worked on (George Gkoutos)
    • How is this supported in MGI?
      • Could spit back EQ, but could not allow users to search
  • MGI isn’t in a position to use EQ internally, but for example Phenoscape II could provide an EQ-view on mouse phenotypes, using the decomposition of MP into anatomy (or entity) and quality term cross-product
  • Full EQ annotation for OMIM is being planned but not yet funded
  • MGI, Xenbase, and ZFIN all have links from their phenotype data to OMIM
• Phenoscape II: Development of anatomy - new queries supported; would generate testable hypotheses; how exactly do those queries rely on developmental data?
  • Different approaches between MGI and ZFIN:
    • MGI uses complete anatomy at different developmental stages
    • ZFIN uses one anatomy ontology and adds start and end dates to indicate the developmental period during which it appears (adult structures don’t have an end date)
    • Xenbase uses the ZFIN approach
  • Candidate genes for evolutionary change could be derived from anatomy-annotated gene expression studies during development; Where do mouse and Xenopus share gene sets in early development?
    • genes responsible for or associated with morphological changes during individual development could be candidates for evolutionary change
    • evolutionary phenotype changes could be used to query morphological changes during development
  • Can we enable queries to generate hypotheses based on ontogeny reflecting evolutionary history?
  • Powerful tool in interpreting microarray data downstream from node; know candidate genes without mutants using this approach
  • See phenotypic differences between 2 taxa – where do you see similar changes?
  • Cell types and associate with time and space – can reason from, neural crest, etc.

• • Evolutionary developmental data could come from medaka, stickleback
• Sequence of steps:
  1. Ontology building
     • Adult phenotype annotations for mutants in Xenbase
     • Presently only 3 species for amphibians: Xenopus, Dermophis, Salamandria (integration beginning in July; phenotypes/mutants, adulta; L. Zimmerman (GB))
     • Development decoupling from anatomy ontology in mouse (as per above)
       • Requirements:
         • QC required – 1 person to find orphans and generate reports (80% complete); make decisions
         • 1st: alignment of MP and mouse anatomy, then QC of MP-EQ; use Mouse anatomy to initalize Paul’s ontology
         • 2nd: Mouse staging-> ZFIN + Xenbase style
         • Phenoscape II: Time required for above (1st and 2nd) is 1 person over 3 years
     • Expanding mammalian anatomy to include extinct species
       • • Judy mentioned Fiona McCarthy (chick ontology? Judy will ask)
     • Anatomy for amniotes (the clade including mouse and dinosaurs), including extinct taxa (such as dinosaurs)
       • Scope of this could be overwhelming
       • Should be strongly driven (or staged) according to the character matrices to be annotated
       • Chicken anatomy could provide a starting point?
       • There is work on bird anatomy that uses a latin naming scheme
       • Work on any smaller-scope anatomy (or multi-species anatomy) ontology will contribute terms that apply more broadly
       • There may not be very many neomorphs between birds and mammals, though there are a few areas such as the digits in birds where the exact homology relationships aren’t as clearly agreed upon.
       • set up ontology and extend to fossils that Paul knows best;
       • also need taxonomy onotlogy (from suprageneric filemaker database?)
  2. Mammalian phenotype decomposition
     • Need support for QC’ing the results of automated decomposition
     • Alignment of MP with mouse anatomy
  3. Annotation
     • Which published character matrices are there for dinosaurs?
• Ontology mapping and alignment
  • Need to align teleost and amphibian anatomy to mouse.
  • Mouse and chicken need to be mapped to amniote anatomy. Mouse is a better start because there are genetic data.
• Paul Sereno gave short presentation on reconciling character-derived trees and character definition and use between different matrices and trees that share taxa
  • TaxonSearch
  • Formalizing and generating grammar of character coding and character state definition
    • Phenoscape II grant activity could be to produce EQ primer
  • presented summaries of annotations, by region, by authors, by structure, by quality
  • Paul’s question: Why are 2 trees different? A: Particular characters and types of coding; If you are trying to develop a consensus tree – can see how authors’ differ
  • Analyzing character usage (shared, not shared, rejected) between trees that share taxa
  • Conflicting phylogenies for the same set of taxa often turn out to be based on character codings that are not consistent or not compatible
  • need to not only curate legacy data but be proactive in terms of syntax etc. of future data; use cases looking forward; morphology in crisis, wallowing in a sea of data
• Re: direct submission –Monte: ZFIN has 6,000 users, but 4-5 labs do direct submission of a lot of data; he suggested Phenex modified as a web tool to put in data; also ontology modification/use of Mesquite

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• Miscellaneous discussion following above (Tuesday pm)
• Open to communities
  • Phenoscape has public data, but can upload private data and use visualization tool
  • working environment enabling exploration of data for analysis
  • would allow people temporarily to overlay on whole data store

• NCBI blast similarity – phenoblast
  • Will need term tracker
  • Monte: Issue of best practice for global size/shape
  • Todd: (here is forest of EQs that match)
    • can move up and down ontology
    • shape and syntax; best practice

• Discussion of images (linked to AO, PATO) – definitional, put in ontology; browsing, finding right AO term
  • could call for images in particular sets of species

• Are ontologies useful for phylogenetics? ATOL data and relationships are a challenge (Paul)
  • Can a matrix be reconstructed and can data be related in an effective way?
  • Do ontologies serve this community well?
  • Limiting from community?
  • Explore whether useful for phylogenetics?
  • Capability of characters for phylogenetic studies?
• Viability of PhenoscapeII depends on morphologists using it!
  • vast phylogenetic branches – does character annotation at gross level conceal or reveal phylogenetic information?
  • Can we retrieve the characters that are discordant?
• What question motivates character matrix?

Developmental time & misc discussion

• Development of mouse and Xenopus:
  • Notochord in adult example
• Phenoscape II: create developmental time ontology for vertebrates.
• Compare heterochronies:
  • relative ordering of entities and associated gene expression
  • Anne’s example of heterochronic frogs…

• • Notochord-hedgehog at particular times & wnts
• For a given evolutionary change, what are genes expressed in a time at a place?
  • pick ~ 12 terms and make table and map for multiples species

• Phenoscape and vertebrate development ontology (?)
  • would facilitate finding genes responsible
  • without start and stop times, would have develops_from only
  • enables placement of a phenotypic information into a developmental framework; develops_from
  • what are the sets of characters that evolve at derived condition; see how phenotypic characters cluster at particular branch points; even do math, counting nodes; can do stats at branch points.
  • creating diff definitions of homology; try to experimentally differentiate species
• Evolutionary time: use cases; compare sister groups
  • Rates
  • Dating clades – minimum age

• Database discussion – Todd/Jim

• OBD – Suzi – Need to work on ability to pull things back on basis of similarity; on basis of phenotype – what else is there that affects a bone?
• Suzi & co. would adopt single searches by gene or body parts

• • Cartik: Support units and measures
  • Jim: User see OBD structure – enter a term and visualize EQ annotations in relation to it;
  • See Ensemble – Phenoscape Mammals; Phenoscape Amphibs; Phenoscape Fishes – Allow user to move between taxonomic stashes without mapping

• • Sparkle: Chris: issue generic queries – return data in generic format

• • Suzi: Allow people to add term if they are making query and not finding anything
    • could repurpose protein tree/ GO
    • relative ordering of entities and associated gene expression

Wednesday morning, April 29, 2009

• Expanding taxonomic coverage to Vertebrata
  • Phenoscape has about 15,000 species of teleosts untouched (half that number is sampled in a typical study) and approx 200 matrices to target
  • Amphibanat estimates 3,000 amphib species and approx 36 matrices
  • Plan to maintain skeletal focus for anatomy development
• How best to keep nomenclature history?
  • Nomenclatural history of terms in ontologies
  • mechanism to keep track of in OBO-edit? No
  • keep track of this information on the database side
  • Current exchange format standards don’t support this really beyond obsoletion
  • ZFIN tracks within the database the complete nomenclatural history of gene names; (ZFIN records the reason, comments etc…in database comments)
  • RDBOM tracks literature and author attribution for anatomy terms but not yet nomenclatural history
    • Amphibanat handles comments with fields:
      • Is_defined_by:
      • Is_discussed_by:
      • Literature citations are an ontology linked to other concepts
• Character quality profiles for data matrices
  • Addresses the question of “Where in the skeleton are the changes occurring that drive the phylogeny”
  • Distribution of characters across the skeletal anatomy, at different levels of the hierarchy
  • Distribution of missing data across the anatomy, at different hierarchy levels
  • How many taxa have how much missing data, distributed on which anatomical parts
• DRIVING QUESTIONS:
  • What parts are of phenotype are variable a) in particular taxonomic groups; b) in particular author’s studies?
    • Where are the gaps in character variation? In taxon sampling?
    • Why are there gaps in phenotype variation? Missing data, fossils
    • What is not changing – not in matrix –
    • Because extinct not in fossil record (no a??)
    • Or constrained (just no variation)
    • To get at redundancy, have to factor in taxonomic sampling and character sampling.
  • Q: Who much is good data? How much is redundant?
    • What is redundancy? Identical EQs? Action: curate to fine grain in order to match; develop tool to be able to see other EQ annotations
  • Q: How does the order of development correspond to the order to evolution?
• Use case: Character redundancy
  • Deriving a character profile across the anatomy could help visualize the redundancy between annotations
• Use case: Mapping the evolutionary characters that lead (and distinguish) to a model organism. Subsequently, see whether these evolutionary changes and the order in which they appear to the ontogeny of the organism.
  • Will need to deal with character gaps and with character redundancy for this.

Specific goals:

1. Expand taxonomic coverage of Phenoscape to Vertebrata
   • Mouse is done but needs to be rearranged (MP decomposition)
   • Amniotes need to be done from the ground up

Wednesday afternoon

• Problem of lossy transformation of legacy character data
  • EQ annotation is often at a lesser granularity (or level of detail) than the original free text description
  • This isn’t due to any technological obstacles but rather due to the limited resources available for annotation.
  • Annotation effort is best focused to a granularity level where it suffices to solve a use-case of interest.
  • Annotating at very granular levels is entirely possible but can take a lot of time because many of the ontology terms needed are likely not to be present yet in the ontology.
  • How does this impact phylogeny and data matrix reconciliation, or phylogenetic reconstruction on the basis of the EQ annotations?

• Use-case for development
  • Heterochrony would be interesting if one can pull it out of the database
  • Ordering of developmental landmarks uses develops_from; Developmental ordering relationships currently used are confined to develops_from and transforms-into.
    • This is missing yet for mouse.
    • Wouldn’t really allow inferring heterochrony.
    • Would allow though to place and compare the placement of phenotypes into a developmental chain of transformations.
  • Use case to compare sequence of ossification in ontogeny of an individual vs. among species variation in degree of ossification of a structure; idea is to visualize where these structures are on the developmental sequence of a MOD
  • Homology and develops_from:
  • Juvenile wing primordiium homologous to adult limb?
  • John: should add the phrase to any homology statement: “two things are homologous as _______”

• Evolutionary time:
  • TimeTree www.timetree.com; pairwise comparisons to get ages
  • Questions that can be asked regarding geologic time:
    • How far back in time do you need to go to find a particular change in phenotype?
    • Does this type of character change occur during a particular time period?
      • Requires trees

• Informatics: what do you want to see?
  • Cartik: measurements displayed in web interface (it’s supported in Phenex and OBD currently)
  • Jim: user upload; group annotations and click through neigborhoods…see Hilmar notes

• Tree visualization
  • Nodes don’t have ancestral state reconstruction, they are the union of phenotypes in the database; displays all the phenotypes that are recorded in a clade, not mapping of characters.
  • PhyloWidget developed in 2007 summer of code
    • Annotate parts of the tree with images, phenotypes, etc.. to a tree topology
  • Character optimization for Phenoscape II
    • Optimizing EQs involves deciding which EQ is alternative to another
    • Todd: Easier for user to download data and create matrix on their own

• Phenex stuff:
  • Add skeletal parts in association with museum voucher for paleo data; for extant dry skeletal vs. cl/st. Could help discern WHY, e.g., cartilage is not variable in data matrix.
• Demonstration of Phenoscape KB
  • Some of the features we are developing (the 3 principle queries) would be very useful to MOD users
• Informatics goals for Phenoscape 2:
  • Supporting units for measurements
  • Allowing others to compare their phenotype data to the knowledge base
  • Generic ontological queries, such as a SPARQL endpoint
  • Private data overlay
  • Linked Data and semweb integration
  • Tree visualization
  • Triple store technology evaluation
  • Species ID
  • Phylogenetically informative distance metric based on EQ assertions
  • NLP-based text processing, Mass curation

Idea bin

1. Intermine connection (multiple model organisms, AJAX-based widget for displaying protein family tree)
2. Some phenotypes imply developmental abnormalities, differences, or variation.
   • For example, a “poorly ossified cranium” in an adult amphibian implies that the developmental process was delayed or did not complete.
3. How does logical inference of homology propagate over develops-from relationships.
   • E.g., if A and B are asserted homologous, and C develops from A and D develops from B, are then C and D inferred as homologous, and are C and B inferred as homologous.