These synonyms can now be used in searches of the Phenoscape Knowledgebase. For example, you can see the French synonyms for ‘paired fin’. One can imagine ultimately being able to select a preferred language or term label when browsing the ontology in the Knowledgebase.

These were the first set of foreign terms to be added to the teleost ontology, and we had to tweak the Phenoscape Knowledgebase interface to display the diacritical marks correctly. We are ready to accept more! Please send me anything you’d like added or changed to the TAO term tracker.

[1] Chanet, B., & Desoutter-Meniger, M. (2008). French-English glossary of terms found in Chabanaud’s published works on Pleuronectiformes. Cybium, Electronic Publication no 1:1-23. PDF download

Of particular relevance to our poster was another presented by Cam Webb. Cam has created an OWL-compatible version of Darwin Core which can be used to describe specimen metadata in RDF. We made similar use of Darwin Core in our poster, but we are looking into adopting Cam’s Darwin-SW for this part of the model.

Overall there was a lot of interest in semantic technologies at TDWG, ranging from the initial meeting of an RDF/OWL working group to other projects that are not using semantic technologies but seem well suited for RDF.

We used the Synchronization Tool (an Obo-Edit plugin) to compare XAO to several external ontologies. The tool made it efficient to find and add missing cross-references and terms, and to resolve conflicting data (e.g., differing definitions). By the end of the week, we updated XAO with all relevant terms from the Amphibian Anatomy Ontology (AAO), Vertebrate Anatomy Ontology (VAO), Uber Ontology (UBERON), and Common Anatomy Reference Ontology (CARO).

Erik, VG, and Christina worked hard the rest of the week to make XAO is_a complete and to update definitions, relationships, and synonyms for existing terms. With XAO’s new release, the ontology is now 25% larger than before. The newest version of XAO will be available for downloaded soon from the OBO Foundry.

We presented talks at the Facilitating Anatomy Ontology Interoperability workshop. Jim’s talk was on representing taxa as individuals in OWL, an alternative to the common representation of taxa as classes, which facilitates annotation of phenotypic data involving polymorphism and evolutionary reversals.  I presented a lightning talk on the anatomy ontology synchronization requirements for linking evolutionary and model organism phenotypes.  Other presentations from the workshop are available here. We also presented a poster describing the reasoning used in the Phenoscape Knowledgebase.

The main conference included interesting talks on a broad range of topics including the application of ontologies to proteins, diseases, biological mechanisms, and electronic health records. Presentations can be downloaded here.

The first issue is that we are interested in changes in phenotype, not simply matching phenotypes.  For phenotypes associated with mutants of model organism mutants, it is understood that they vary with respect to the wild type.  For taxa, however, this means looking for taxonomic nodes where variation in a phenotype is observed among the children of the node.  For example, there are nine species within the genus Aspidoras with annotations for the shape of the opercle bone.  Of these, eight exhibit opercle bones with round shape, but the ninth (A. pauciradiatus) is annotated with a triangular opercle.  In contrast, all three annotated species of the related Hoplosternum are annotated with a triangular opercle.  Thus there is detectable variation in opercle shape within the children of Aspidoras, but not within  Hoplosternum - suggesting that change in opercle shape has occurred somewhere among the descendants of  Aspidoras. For our analysis, identifying variation among descendants is important.

Thus, our search for shared variation in phenotypes focuses on matching phenotypes associated with genes with phenotypes of taxa showing variation.  However we are looking for matches at a larger scale than single phenotypes; we are looking for matches across the set of phenotypes affected by a gene or the set of features that have changed among the descendants of a taxonomic node.   We refer to these sets of phenotypes as the ‘phenotypic profile’ of a gene or taxon, following a seminal paper by Washington et al. 2009.  Washington et al. propose four metrics (three based on ‘information content’) to score matches between the sets of phenotypes in a pair of profiles.

In the course of developing the search, we have encountered several important differences in curation approach between ZFIN and Phenoscape.  In some cases tehre are different uses of PATO to model the same phenotype, for example the absence of an entity.  In other cases ZFIN uses a quality ‘abnormal’ that applies to mutants, but not in a taxonomic, comparative sense, which means these phenotypes will be inaccessible to us.  Thus, implementing this search is helping us to better understand our data and our choices in modeling the data and how it interoperates with other ontology-based data.  Such reflection would have been difficult or impossible without the use of ontologies to represent the phenotypes.

Some proposed changes to PATO:

• Consolidate relational and monadic branches: One of the more major decisions was to remove the distinction between the “relational” and “monadic” branches of PATO. The relational terms can be descendants of the monadic terms which are pre-composed with a reference to a dependent entity. This change would be a major improvement helping to relate terms dealing with similar concepts and for inference using these concepts.
• Continuums: Add a relationship ‘ranges_from’ which can be used to specify a continuum of values between two indicated qualities.  Example: a color grading “from yellow to brown”.
• Position: Remove term ‘position’ after moving its children to more appropriate places.
• Enable directional references: Add classes describing directions a structure can be pointed.  These classes should include pre-composed logical definitions drawing on the spatial ontology. An example would be ‘directed posteriorly’.
• Spatial term review: Review all existing PATO terms referencing spatial aspects, and verify that they are based on logical definitions using the spatial ontology.
• Size vs. shape: Several children of ‘size’ were noted to actually be types of ‘shape’. Many of these were noted and several were immediately revised by George Gkoutos.  This discussion revealed that many free-text characters defined by biologists refer to size-sounding terms when they are actually describing changes in shape.
• Changes in various term definitions:
  • PATO:1485 should be obsoleted and two new separate terms, ‘condensed’ and ‘compressed’ (as a synonym of ‘flattened’) should be added. ‘Condensed’ is considered to be a type of ‘structure’, while ‘flattened’ is a ‘shape’ instead of a ‘curvature’. All children of ‘flattened’ should be reviewed to remove references to ‘curvature’.
  • Improved definition for ‘morphology’ referencing “shape or size or structure”.
  • Clarified terms ‘surface feature shape’ and ‘texture’. The parent term ‘surface shape’ was obsoleted while ‘surface feature shape’ is retained as a shape with a repeated feature on a surface. A ‘has_repeated_part’ relation should be added to be used in pre-composed subclasses of ‘surface feature shape’, linking them to specific shapes.
  • Add a term defining ‘spatial density’. The existing ‘density’ term refers to the physics concept.
• Spatial pattern: We proposed reworking the ‘spatial pattern’ term hierarchy to logically reference other terms which the given pattern is in respect to (structures, colors, etc.). The ‘color pattern’ term should be moved under ‘spatial pattern’.
• Synonyms: We discussed some community-specific term labels for various PATO classes.  There is an existing OBO standard for how to implement these as synonyms. Community-specific applications would need to support display of the appropriate synonym.
• Comparative relations: Generalize existing comparative relations in PATO.  For example, Instead of ‘increased_in_magnitude_relative_to’, it will be ‘increased_in_value_relative_to’.
• Qualitative branch: Clean up and better document ‘qualitative’ hierarchy (which is used for various logical “shortcuts”).

EQ representation issues:

• Size bins: Relative size characters (small, medium, large) can be represented by creating (within a given annotation application) anonymous subclasses of size which are related to each other in the appropriate way using relations such as ‘increased_in_magnitude_relative_to’.  This will provide the appropriate relative size inferencing for the given character states, but, as in the original paper, not be readily comparable to size classes created for characters in other studies.
• Negation: When describing a phenotype that is simply “not something else”, e.g. ‘not round’, the complement_of operator should be used in an OWL class expression.
• Comparative/relative qualities should not be conflated with relational (or, better, dependent) qualities. Comparative relations such as ‘increased_in_value_relative_to’ can be used to relate one EQ to another.
• Phenex and other annotation tools should provide enhanced interfaces for these special representation issues: creating comparative EQs by simply entering a relative entity or taxon, a simple means to say things like ‘not round’, and a way to create local groups of relatively ordered qualities for a given character (e.g. small, medium, large).

The second day focused on applications to biological data and web services.  A discussion on “taxonomic intelligence” was particularly illuminating.  It provided an example of how different communities can share a set of identifiers for species, for example, yet provide their own set of statements about the taxonomy relating those species.  Each community can draw conclusions relevant to its preferred taxonomy using data associated with the same species.

The afternoon focused on the SSWAP project, led by Damian Gessler.  SSWAP is a protocol which uses OWL documents to describe the inputs and outputs relevant to a web service.  Interestingly, users of these web services would submit their input in the very same OWL model used for service descriptions.

In Phenoscape, we are using OBO ontologies rather than RDF and OWL and storing our ontological annotations in OBD, a datastore tailored for OBO technologies which provides its own very effective reasoner.  However, this workshop provided a great opportunity to stay up to date with semantic web standards and explore how to make our data compatible with and part of the global semantic web.  In addition, St. John’s College was a great meeting location – it is a small college with a wonderful natural landscape in the hills outside of Santa Fe.

Open access links to online versions of the paper are given below:

Wasila M. Dahdul; John G. Lundberg; Peter E. Midford; James P. Balhoff; Hilmar Lapp; Todd J. Vision; Melissa A. Haendel; Monte Westerfield; Paula M. Mabee.  2010.  The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age.  Systematic Biology.  View full text or download PDF.

As an online student of Bioinformatics based in Nairobi, Kenya, I had a strong desire to undertake a project that would enhance my knowledge and skills in software development. Hence, after completing MSc. Course work at the University of Manchester, UK, I was happy to be awarded an internship from the Phenoscape project for an 11-week traineeship beginning September 21^st, 2009 at the National Evolutionary Synthesis Center (NESCent). This project seeks to establish the developmental and genetic basis of the astonishing morphological heterogeneity across diverse species. In addressing this, a rich and rigorous knowledge base, PhenoscapeKB, constituting evolutionary variable characters across a clade of fishes connected to mutant phenotypes from ZFIN has been developed. Core to the PhenoscapeKB is the modeling of the character entities   using ontologies thus facilitating the knowledge synthesis via logical/mathematical reasoning.

During the internship, I successfully developed a Java-based prototype application for handling ontology term requests, gained in-depth skills and knowledge in software development, made two presentations to the informatics group and above all established a long-term collaboration with the Phenoscape project team.  I am currently working remotely with the team (via Skype and e-mail) and developing my MSc. thesis under the close supervision of Prof Todd Vision (the UNC co-PI in the project). In addition, based on the knowledge acquired during the traineeship, I plan to conduct a basic course in bio-ontologies and Java programming for bioinformatics for members of the regional student group of East Africa in mid 2010.

The traineeship provided an open and stimulating learning environment sustained by the weekly seminars, journal club presentations and the informal yet fruitful discussions. The constant willingness of project team members to guide and share knowledge and above all, the scientific mentorship was profoundly motivating.

I must say that the traineeship provided the best learning experience I have ever had and will go along way in shaping my career in Computational biology.

Regards,

Mtakai Ngara

International Institute of Tropical Agriculture (IITA), Nairobi, Kenya

While the rest of Phenoscape was at the ASIH meeting, involved with the ontology workshop and the release of the database and website, I was across the country, representing Phenoscape at the International Conference on Biomedical Ontologies (ICBO) in Buffalo, NY.  ICBO covered 2-3/4 days (July 24-26) of presentations with two evening poster sessions. There were also software demos during the lunch breaks, and two panel discussions.

Although many of the sessions were devoted to ontologies of disease and clinical practice, there were a number of talks of interest to Phenoscapers. Among these were several alignment talks, including one from the BGEE group on Homolonto and Chris Mungall’s on GO cross products and Uberon.  There were also sessions on annotation and natural language processing (NLP), including Mike Bada’s talk on developing a corpus for testing NLP based annotation. There were also two talks specifically about ontologies and physiology, one by John Gennari focused on integrating existing anatomy ontologies (e.g., FMA) with physiological simulations, though he specifically ducked ontological modeling of physiology as process.  The other was an ‘old school AI’ simulation of a patient, that includes models of physiology, cognition, and NLP.

There was also some promising activity on behavior ontologies, including a poster by Tim Beck, a postdoc from the UK on a mammalian behavior ontology and a “behavior lunch” on the second day, with Tim, Judy Blake, David Shotton (ABO collaborator from Oxford), Mary Shimoyama (RGD), and several others.  There is a European plan to develop a new OWL-based general behavior ontology, and Chris Mungall has recently established an OBO-behavior list.

There was also a lot of discussion generated by the proposed ontology of homology relations, although the consensus from the numerous people I discussed it with was that it needed more work.

Other interesting ontologies included an ontology of Evolutionary processes presented in a poster by Adam Goldstein (Iona University).  He’s since been in contact with Hilmar, and I believe with representatives of CDAO and Dryad.  Phenoscape was also represented by a poster.

There were two panels, one focussing on Ontology and Publishing.  Although the lineup, which included a representative from Elsevier (Jabe Wilson) and Alan Ruttenberg from Science Commons, suggested a discussion on open publishing, the Elsevier representation was quite restrained, and it was Larry Hunter who made the strongest argument that publishers currently provide little value to academics.  David Shotton discussed his semantic annotation of a randomly selected paper on a tropical disease, and there seemed to be consensus that semantic markup ought to be either the author’s or the publisher’s responsibility, rather than the current post-publication markup by project curators.

The second panel was on the future (and past) of ontologies and knowledge representation.  I think the two memorable claims from this discussion were the call to expand the A-box (since the T-box is really less than most people think) and Barry Smith’s claim that in 25 years consulting ontologists will be as common in biology and medical departments as statisticians are today.

The text from all the presentations and posters will be made available at Nature Proceedings.  There was also an ICBO group on FriendFeed with other attendee’s tweets from the conference and preceeding tutorial sessions.  Finally, I will be posting a more detailed report on my personal blog.

There is another phenoscape ontology that would benefit from the use of individuals: our ontology (ok, it’s really a vocabulary) of research collections of fish. Part of our process for curating anatomy papers involves constructing a list of all the specimens reported in the paper (generally the author includes this in the paper, but we enter it to facilitate annotation). The specimen lists consist of collection names and numbers. Although research collections are supposed to have standardize names and abbreviations, practice does not always reflect these standards: the same collection may be abbreviated in different ways by different authors, and collections occasionally merge and the smaller collections might disappear into larger ones or be renamed.

So we constructed a vocabulary of fish collections with their 4-5 letter abbreviations, longer name and possible synonyms. Now a research collection contains individual specimens, but these are parts of a collection, not subtypes of a particular collection, and therefore, the collection is best represented as an individual, not a class. So, the collections vocabulary, represented as an OBO ontology, should ideally use OBO instances (which exist to represent individuals), rather than terms for the collections.

Unfortunately, the current version of OBO-Edit, although it will read and save ontologies containing Individuals, provides no facility for either viewing or editing these individuals. Furthermore, although there are several OWL editors that would allow us to work with Individuals, there are no OBO<->OWL translators that understand what to do with OWL individuals, so they are just omitted in the OBO translation, even though the OBO file format, since version 1.2, has supported Instance ‘stanzas.’

Several of us recently discussed this issue with Chris Mungall, who mentioned a similar issue with the GAZ ontology of geographical terms, though the developers of GAZ are not as concerned as we have been with the Individual/Instance vs. Class/Term distinction. Since adding support for Individuals would impact the final release of OBO-Edit 2.0, which we all want, and as an OBO-Edit plugin was considered too risky (e.g., would likely introduce difficult to detect and fix bugs), Chris proposed an ‘out board’ solution.

This solution would involve adding an instance_of relation to any ontology that wanted to use individuals. Although instance_of is not one of the ten relations listed in the published OBO relations ontology, it is defined as a primitive and used throughout Smith et al. (2005).  Entities that were intended to be individuals would be defined as terms, but rather than link to their parents though is_a relations, they would use the locally defined instance_of. The out board tool will be able to convert OBO stanzas that linked to parents through instance_of back and forth between term stanzas and instance stanzas. With term stanzas, individuals would be syntactically classes, but visible to OBO-Edit, whereas when they were instance stanzas, they would be correct, but invisible to current versions of OBO-Edit. Eventually, OBO-Edit and its reasoner(s) will include support for individuals.

This seems like a workable solution and the best we can expect given current limits of time and people.

We need to especially thank all our speakers for their excellent presentations, They not only gave the audience a varied introduction to ontologies, but also a set of examples of the integrative questions that can be answered using them.   The slideshows for all of these talks are on our wiki but I thought I would provide a brief overview of each one right below as a summary of the workshop. The use of ontologies is just emerging in evolutionary biology, and it is an exciting time to be involved in this field.  As we move forward to use ontologies in evolutionary biology, we discover new requirements and challenges — for example, the challenge of how we create ontologies that are interoperable — so that we can ask big questions that span not only taxonomic groups (such as bees and fishes and mouse and fly) but different knowledge domains (such as phenotype, evolution, and genetics, genomics, medicine).

So here is an overview of each talk.

Barry Smith (NCBO and Univ. Buffalo) kicked off the workshop with “An Introduction to Ontology for Evolutionary Biology“.  He talked about the GO in relation to “doing biology across the genome”, and he described the domain coverage of the ontologies in the OBO foundry.  He introduced basic ontological concepts and relations, including several new ones that must be made in creating ontology resources for evolutionary biology.  He is currently working with a number of groups including EoL to develop an Environment Ontology (EnvO).

Chris Mungall (Lawrence Berkeley Labs) presented “PATO: The Phenotype and Trait Ontology“.  He focused on why we need ontologies (for example, to solve the data integration problem), introduced “phenotype” and the newly proposed Homologous_to relation. 

Monte Westerfield (Univ. Oregon, Zebrafish Information Network) talked about the use of ontologies in “Linking Animal Models and Human Diseases“.  Just as BLAST can be used to connect animal genes to human genes, shared ontologies and syntax can connect mutant phenotypes to candidate human disease genes. He talked about the importance of curation consistency and how it can be measured and increased.  His proof of principle example, comparing ontology-annotated phenotypes in human and zebrafish demonstrated that genes associated with human diseases can be identified.

It was then my turn to introduce Phenoscape in my talk “An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics“.  Just as animal model phenotypes can be compared to human phenotypes using ontologies, so can animal model phenotypes be compared to phenotypes of multiple species – thus linking comparative evolutionary data to model organism genetics.  I presented several use cases for fishes and described the rapid progress that we have made in developing new ontologies, extending existing ones as well as some of the challenges involved in multispecies ontologies.

Jim Balhoff (NESCent, Phenoscape) presented the software that he has developed for curation of evolutionary phenotypes “Phenote: Curation Software for Evolutionary Phenotypes“.  Originally developed for ontology-based annotation of genetic mutant phenotypes and widely used by model organism curators, Jim described how he has extended and reconfigured Phenote to handle comparative evolutionary data, and he also spoke about his plans to integrate ontology-based phenotype descriptions into the NeXML file format.

Melissa Haendel (Zebrafish Information Network) presented “The Common Anatomy Reference Ontology (CARO) and queries across species“.  She described current anatomy ontologies and why we build them, and the standardization and integration of anatomy ontologies using CARO.  She explained how the issues created by homology can be addressed, including the draft definition of the Homologous_to relationship, and she described how homology data can be used with ontologies to query across species. 

After lunch we had about a ½ hour of “Lightning Talks” during which workshop attendees had an opportunity to introduce themselves and give brief (2-3 minutes) descriptions of their interest in ontologies.  Several attendees seized the chance and made the audience aware of their ontology building efforts.

After that, Ann Maglia (Missouri Univ. of Science and Technology, AmphibAnat) resumed the regular talks and spoke about her group’s work in the “Development of the Amphibian Anatomical Ontology“.  This ontology was driven by the need of the amphibian community to standardize their terminology and thus integrate their comparative work.  She is exploring automated techniques to reduce manual efforts and enhance existing, manually created ontologies.  Ann also described the relational database (RDBOM), the modularization, and web-based community curation methods built by her group and community. 

Martin Ramirez (Museo Argentino de Ciencias Naturales) in his talk “Ontologies, Image Databases, and Evolutionary Biology” described the use of the spider ontology to link images from the spider Tree of Life project to a phylogenetic dataset and a body of image annotation.  He discussed a series of challenges, such as issues involving the alignment of ontologies using homology relations and the “combinability” of ontologies.

Todd Vision (Univ. North Carolina, NESCent), presented “Ontologies and the Identification of Candidate Genes for Complex Traits“.  He considered the qualities of “good” candidate genes and how they are typically discovered and ranked, and then described a test case where ontology terms were used in picking candidate genes computationally (using an approach named CAESAR) for Type 2 Diabetes.  This approach has a promising application for evolutionary traits in non-model organisms.

Peter Midford (Univ. Kansas, Phenoscape) introduced taxonomy ontologies with his talk “Names, Ranks, Clades, and Taxonomy Ontologies” — what’s in them, how they are built and why one would use one.  The issue of what species are ontologically, more specifically whether species are classes or instances or both, impacts not only the way an ontology is built but also what kinds of assertions can be inferred or not.

Suzanna Lewis (Lawrence Berkeley Lab, BBOP) and I wrapped up by listing some of the challenges for the evolutionary biology community that became apparent over the day. 

Especially prominent was the need for communication among evolutionary biologists developing ontologies so that they can be developed from the outset to be interoperable.  This and many related comments from attendees suggested that an NSF-RCN (Research Coordination Network) proposal might be the best next step and an effective mechanism to fund and promote communication among and between evolutionary biologists, ontologists, and model organism biologists.

As a result, we are now beginning to gather ideas, objectives, and possible participants for an RCN proposal. If you have thoughts on this, or if you are interested in participating, we would love to hear from you – leave a comment here, or email me (pmabee{at}usd{dot}edu).

Peter Midford and I recently attend the two-day Relations Ontology workshop in Denver, Colorado. The goal of the meeting was to further develop the Relations Ontology (RO) by moving relations from RO proposed (ontology for relations yet to be officially added to RO) to RO, and adding any new relations proposed by attendees. Impressively, almost all of the items on the original agenda were covered, and an ‘action list’ was produced to focus efforts subsequent to the meeting.

Phenoscape had several relations on the agenda, and Peter and I have summarized the discussion, definitions, and examples used.

On Monday afternoon, Wasila and Peter presented proposals for the following relations for the section organized by Suzi Lewis and Melissa Haendel on spatial relations:

1. Overlaps

Peter presented examples and definition for overlaps. Overlaps is particularly useful for Phenoscape so that we can represent a joint without having to create new terms for the parts of bones that participate in the joint. We can simply say, for example, that bone X overlaps joint XY. After brief discussion, it was decided that this relation will be added to RO with the proposed definition.

Examples:

bone overlaps joint

axon overlaps axon tract

definition:

X overlaps Y =def. for every t and every x, if x instance_of X at t, then there is some instance y of Y at t such that (x overlaps y at t)

where

x overlaps y at t =def there is some z such that z is part_of x at t and z part_of y at t

Note that it can be the case that X overlaps Y as thus defined, even though Y does not overlaps

2. Attached_to and connected_to:

Wasila presented examples of these two relations and definitions given by the FMA (although the FMA definitions are reversed from how we use them in our use cases). There was discussion of whether or not it is useful to distinguish between fiat and bona fide boundaries, whether a single “connected” relation could suffice for all use cases, and whether a force-connected definition would be better to use. However, the overriding point was that biologists clearly make the distinction between attached and connected, and it was decided that attached_to and connected_to would be added to RO pending development of their formal definitions.

Examples:

tooth attached_to bone

muscle attached_to bone

axon connected_to neuropil

3. Spatial Ontology

Wasila presented examples of how Phenoscape uses the Spatial Ontology, and much discussion centered on how to improve this relatively new and little used ontology. Some classes (e.g., anatomical region, anatomical surface) should be moved to CARO, and reference images would be helpful in providing examples for the different anatomical axes.

Homologous_to relation

We presented a proposal for homology relations on Tuesday morning. Melissa started with a couple of background slides and Peter continued with a presentation of the definition we developed as a group on Monday night. That definition was revised again on Tuesday afternoon and the Tuesday afternoon revision can be found below. It, along with earlier revisions is available on the wiki page (http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_homologous_to_relation).

Directly_descends_from – This is currently defined as follows

Example: Child’s arm directly_descends_from parent’s arm

definition:

x1 directly_descends_from x2 iff there are y1, y2 such that:

• y1 is an organism
• x1 is an anatomical structure
• x1 part_of y1
• y2 is an organism
• x2 is an anatomical structure
• x2 part_of y2
• y2 is a parent of y1
• the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2*.

* This clause still needs some work. Jim Balhoff added the following critique in discussion on the Phenoscape project list:

[Something that jumps out at me in the definition of directly_descends_from:

I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]

Descends_from – This is currently defined as follows:

Example: My arm descends_from ancestral primate forelimb.

definition:

descends_from is the instance level relation which is the transitive closure over directly_descends_from:

A in B descends_from C in D:

For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)

• a part_of b
• a descends_from c
• c part_of d

(Note – B must be a subclade of the clade descending* from D)

Homologous_to – Defined for classes of anatomical structures and clades

Example: Human arm homologous to robin wing.

definition:

A1 in B1 homologous_to A2 in B2 iff exists A3, B3:

• A1 in B1 descends_from A3 in B3 &
• A2 in B2 descends_from A3 in B3

(Note B1 and B2 must both be subclades of the clade descending* from D)

(*In the genealogical sense)

After presenting the definition, Peter presented a number of examples of character optimization – these included a schematic overview and a tree of bilateralians with a reconstruction that indicated that a heart was not present in the most recent common ancestor of bilateralians. There were also other examples that indicated different common ancestors and presence/absence of homology for traditional and Ecdysozoa/Lophotrochozoa-based phylogenies. The presentation finished with a discussion of the homology evidence codes and their use in Phenote.

We are uncertain of the need to include time (e.g., replace the atemporal usage of exists with temporally scoped exists and existed). Fabian suggested that just to be on the safe side we can include time – it’s not useful but it could stop some people complaining and it won’t affect the logic at all.

This definition mentions clades, avoiding the issue of whether taxa are individuals, classes or both.

We will be revisiting these definitions in the future.