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

The 1.0 release of Phenex includes features allowing it to be used for work with any taxonomic group. It can be configured to load any user-specified OBO ontologies, and users can specify the sets of ontology terms available within each type of entry field.  Also, this release uses the latest version of the NeXML schema for its file format, storing ontology annotations in an embedded RDFa-compliant format.

We look forward to working with anyone interested in making use of Phenex with their own data. Phenex is open source software, released under the MIT license.

The two-day meeting brought together diverse PATO users with the goals of establishing best practices for phenotype annotation, familiarizing everyone with the Phenote annotation tool, and discussing strategies for decomposing terms from the Human Phenotype Ontology into Entity-Quality syntax. Participants at the meeting were Sandra Dölken (Charité, Universitätsmedizin Berlin, Human Phenotype Ontology with Peter Robinson), George Gkoutos (University of Cambridge, PATO gatekeeper), Melissa Haendel (ZFIN, data curator and ZFA maintainer), Nomi Harris (BBOP), Sarah Maynard (UCSD, Neuroscience Information Network – NIF, and Protein Knowledgebase Ontology – PKB), Martin Reese (Omicia), Paul Schofield (University of Cambridge, PATHbase and CASIMIR), and Nicole Washington (BBOP).

After project introductions, we started off with software demos and heard about an interesting mix of stand-alone and web-only tools. Sandra demonstrated use of the online Phenomizer and Disease Annotator tools used by clinicians, I demoed the Phenoscape annotation tool (Phenex), and Chris demonstrated queries on Sarah’s annotations loaded into OBD. Sarah also introduced us to Neurolex.org, a wiki-based resource containing NIF ontologies that can be edited by users, with contributions reviewed and added to the ontologies by curators. We then had a discussion of general annotation guidelines, in which I ran through the annotation guidelines we’ve developed at Phenoscape. This led to discussion about unresolved annotation issues including the various ways of representing size, how to refer to one member of a pair (e.g., left and right paired bones), and how to represent an individual of a series.

Following the discussion of curation guidelines, we began the paired-annotation drill of disease phenotypes from OMIM (Online Mendelian Inheritance in Man). We used a special configuration of Phenote that contains a “disease” field for the relevant OMIM disease; “gene” field for known genes; “phenotype” field for terms from HPO, entity field for terms from the Foundational Model of Anatomy, quality field for PATO and Spatial Ontology terms, and free text fields for Age of Onset and Frequency. In addition to establishing curation guidelines for HPO, this exercise resulted in many requests for new FMA terms, PATO terms and synonyms, and feature requests for Phenote.

The relatively short meeting was a good opportunity to discuss the different approaches and commonalities to representing complex phenotypes. The meeting wrapped up with a great meal at Trattoria Corso, followed by a long list of action items prepared by Suzie after everyone returned home.

The ‘5 K Karacters Goal’ was much more ambitious that we realized, resulting in the addition of 205 terms to the Teleost Anatomy Ontology, and more to other ontologies (Phenotype and Trait Ontology, Spatial Ontology, Teleost Taxonomy Ontology). At the end of the curation drive, 4,174 out of 5,445 characters were curated. This resulted in 243,577 phenotypes (unique taxon-phenotype assertions) — now up to 333,987 phenotypes (see tally at kb.phenoscape.org).

A recent publication on Megapiranha paranensis from Phenoscape curators Wasila Dahdul and John Lundberg is in the news!

DURHAM, N.C. — How did piranhas — the legendary freshwater fish with the razor bite — get their telltale teeth? Researchers from Argentina, the United States and Venezuela have uncovered the jawbone of a striking transitional fossil that sheds light on this question. Named Megapiranha paranensis, this previously unknown fossil fish bridges the evolutionary gap between flesh-eating piranhas and their plant-eating cousins.

Present-day piranhas have a single row of triangular teeth, like the blade on a saw, explained the researchers. But their closest relatives — a group of fishes commonly known as pacus — have two rows of square teeth, presumably for crushing fruits and seeds. “In modern piranhas the teeth are arranged in a single file,” said Wasila Dahdul, a visiting scientist at the National Evolutionary Synthesis Center in North Carolina. “But in the relatives of piranhas — which tend to be herbivorous fishes — the teeth are in two rows,” said Dahdul.

Megapiranha shows an intermediate pattern: it’s teeth are arranged in a zig-zag row. This suggests that the two rows in pacus were compressed to form a single row in piranhas. “It almost looks like the teeth are migrating from the second row into the first row,” said John Lundberg, curator at the Academy of Natural Sciences in Philadelphia and a co-author of the study.

If this is so, Megapiranha may be an intermediate step in the long process that produced the piranha’s distinctive bite. To find out where Megapiranha falls in the evolutionary tree for these fishes, Dahdul examined hundreds of specimens of modern piranhas and their relatives. “What’s cool about this group of fish is their teeth have really distinctive features. A single tooth can tell you a lot about what species it is and what other fishes they’re related to,” said Dahdul. Her phylogenetic analysis confirms their hunch — Megapiranha seems to fit between piranhas and pacus in the fish family tree.

The Megapiranha fossil was originally collected in a riverside cliff in northeastern Argentina in the early 1900s, but remained unstudied until paleontologist Alberto Cione of Argentina’s La Plata Museum rediscovered the startling specimen — an upper jaw with three unusually large and pointed teeth — in the 1980s in a museum drawer.

Cione’s find suggests that Megapiranha lived between 8-10 million years ago in a South American river system known as the Parana. But you wouldn’t want to meet one today. If the jawbone of this fossil is any indication, Megapiranha was a big fish. By comparing the teeth and jaw to the same bones in present-day species, the researchers estimate that Megapiranha was up to 1 meter (3 feet) in length. That’s at least four times as long as modern piranhas. Although no one is sure what Megapiranha ate, it probably had a diverse diet, said Cione.

Other riddles remain, however. “Piranhas have six teeth, but Megapiranha had seven,” said Dahdul. “So what happened to the seventh tooth?”

“One of the teeth may have been lost,” said Lundberg. “Or two of the original seven may have fused together over evolutionary time. It’s an unanswered question. Maybe someday we’ll find out.”

********************

The team’s findings were published in the June 2009 issue of the Journal of Vertebrate Paleontology.

CITATION: Cione, A., W. Dahdul, J. Lundberg, and A. Machado-Allison. (2009). “Megapiranha paranensis, a new genus and species of Serrasalmidae (Characiformes, Teleostei) from the upper Miocene of Argentina.” Journal of Vertebrate Paleontology 29(2): 350-358.

Image Credits:
Artwork by Ray Troll, 2005

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.

This is a great improvement to our system of file management. We previously used a server for file sharing, which limited us to saving only the current version of each file.  Aside from version control, SVN has other nice features such as automatic file merging if a curator checks in a different version of a file (which might happen if the file on the repository has been updated by another user since the curator first updated their local copy).  Curators also utilize commit comments to document the edits made on a data file.

A few weeks ago, from Sep 27 to Oct 1, we met in the Black Hills of South Dakota with a group of guest data curators and outside advisors to curate high priority papers, refine the curation workflow and Phenex interface, and evaluate the first prototypes for the web-based user interface to the database. Not only did the workshop end up highly productive (see below), we also had a chance to observe the annual roundup of the largest herd of buffalo in North America, swim in cold Sylvan lake, and see Mount Rushmore one evening.

After participant introductions, the day began with several presentations focused on the utility of synthetic research databases (Monte Westerfield) and the way that phenotype-genotype relationships are handled in model organism databases (Suzanna Lewis, Judy Blake) (for the curious, all presentations are available from the Jamboree agenda page). After a brief description of the Phenoscape data policy (Todd Vision), Jim Balhoff introduced the curation software tool, Phenex, which Wasila Dahdul followed with a hands-on curation exercise that involved using Phenex and associated ontologies to annotate phenotypes (characters) using EQ syntax.

We then paired up our guest data curators with project personnel and got them started.  In order to really focus them on EQ syntax and ontology development, we gave each of our guest curators pre-curated Phenex files containing taxon lists, character matrices and free text character and state descriptions from several important publications authored by the guest data curators themselves or within their area of specialty.

Inevitably, curators spent a significant portion of the time on ontology development.  Many new anatomical and quality entities, along with their relationships and definitions, needed to be added to either the Teleost Anatomy Ontology (TAO) or the Phenotype Ontology (PATO) before characters could be expressed in EQ syntax. In the process of training curators to submit new entities to the term trackers for these ontologies we recognized the need for small, dedicated ontology development meetings (e.g. focused on one anatomical region such as the lateral line system in fishes, or all geometrical or shape qualities).  The better the ontology, the more efficient curation will be.

The curation workflow itself is significantly different in Phenex from the Phenote tool, which we used in the first Data Jamboree. It were the issues brought up there that guided the development of Phenex, and indeed this time we noticed a significant improvement in curatorial efficiency.  We were very pleased that by the end of the workshop, the curators had curated 156 characters (~312 character states) for approximately 150 taxa, resulting in over 45,000 EQ annotations.

One frequent topic of discussion was the depth of annotation granularity to which characters should be curated. For example, many systematic characters pertain to shape, frequently with complex descriptors. These can be curated to a high level (e.g. fin: shape) or to a more granular level (e.g. fin: anterior margin rounded). Judy Blake, one of our outside advisors, pointed out that there is a continuum between use of a structured vocabulary and free text.  A reasonable guideline is to say that data specific to an individual study may not warrant the extra effort with granular annotation and should be left as free-text while data that can be compared across studies should be annotated with ontologies at a rather detailed level.

One observation was that the higher the level of granularity, the more often post-composition is required. The mechanics in using multiple post-composition windows in Phenex was somewhat confusing to guest curators. Another important topic involved the difficulty of not having a universal standard across systematic studies – e.g. descriptors pertaining to size and shape cannot easily be extended across systematic studies. This same issue came up at our previous data jamboree, too. John Lundberg suggested that for comparisons of size within a study, an internal grading of character states (a numbered scale from 1 for smallest and higher numbers corresponding to larger sizes) could be implemented, and this is something that we plan to try.

Following two days of curation, we conducted an experiment to assess curation consistency among our group of curators, and to identify areas where consistency can be improved, for example by better curator training, upfront ontology development, or user interface enhancements. We wanted to determine how often, and for what reasons, curators choose divergent EQ conceptualizations for the same character and character states. Five curators encoded EQ annotations for the same 10 character and state descriptions, using Phenex as the software tool. Immediately afterward we reviewed the results with the group. Notably, only two of the 10 characters were annotated identically among all curators. The reasons for why the other annotations differed revealed different interpretations of shape descriptors, inexperience and unfamiliarity with the ontologies and software, and lack of adequate terms in the ontologies (e.g. shape) as major hurdles towards consistency between curators. Identifying these hurdles helps us to prioritize efforts on visualization tools, ontology development and workflow and Phenex development.

In parallel to the curation activities, we discussed the Teleost Taxonomy Ontology (TTO), taxon concepts, and intermediate synonyms.  Peter Midford has added the intermediate synonyms from the Catalog of Fishes (CoF), but many additional synonyms are present in the literature that must be added. We determined that the need to associate synonyms to their references/publications will require an OBO request for one or more database identifiers. At first we considered using the CoF publication database to generate dbxrefs rather than hunting for DOIs or generating our own, but CoF doesn’t contain many of our publications.  Thus we will need to maintain references and unique identifiers for them in our own database.

In another parallel activity, pairs of participants met with Jim Balhoff and Cartik Kothari  for demonstrations of the web user interface. Jim and Cartik are creating the database and web-application for the research community to explore and query the data. The central gateways for entering the database that emerged from those consultations are querying by gene, anatomy, taxon, or publication. The use case-level query to be implemented first is to find evolutionary phenotypes that match a mutant ZFIN phenotype, or, going in the reverse direction, to find ZFIN mutants for a set of phenotypes that differ between taxa. We plan to be able to demonstrate the first version of the interface at the educational outreach workshop at the SICB meeting on Jan. 6, where we also plan to conduct a first series of usability tests. (For those curious, there was much more feedback and suggestions we received, which we compiled all on the project wiki). 

Working our way towards that meeting over the coming months, we will put into place the first components of a production-level database and a fleshed out query interface. Aside from the software development efforts, we are planning ontology development workshops in small groups in the coming year, for example for TAO and for PATO, and we tentatively aim our next outreach workshop for ASIH 2009. In the meantime, we will need to review our data curation priorities in light of our high priority use cases and proof-of-concept experiments for queries across ZFIN and Phenoscape.

During the past year we’ve contacted taxon experts to suggest comparative systematic treatments and to prioritize them based on generality of taxonomic coverage, authors’ enumeration of characters and a published character X taxon matrix. You can see the 76 papers that we ranked as top priority (“A”) and our curation priority in a publicly available Google spreadsheet and on the graph below. We use this document internally to record the nitty-gritty of our progress. (If you see any papers that we’ve missed, please let us know.)

First things first – we needed a OCR formated pdf of each of the 76 “A” papers. It took a summer of searching, interlibrary loaning and downloading docs from university libraries, the BioHeritage Library, and scanning hard copies of electronically unavailable papers. We completed this work for our “A” papers last week.

In order to populate a database with skeletal phenotypes from many species, we need information on the taxonomic distribution of particular phenotypes (i.e., which species show which phenotype). Using Phenote, the software curation tool customized by Jim Balhoff (NESCent) for curation of evolutionary biology literature, we entered taxon lists for each paper by cutting and pasting from the pdfs into a “Publication Taxon” column and into a “Valid Taxon” column. Where published taxon name was no longer valid, it is sometimes designated as a synonym for the valid taxon in the Teleost Taxonomy Ontology, and was thus replaced. Because some intermediate synonyms are not yet in the Teleost Taxonomy Ontology, taxonomic expertise is still required to find valid taxon name for some of the published names. We have taxon lists for 59 of the 76 papers; many of these still require expert review.

Character X taxon matrices make the association between taxa and character states. To save time required for manual entry, we contacted authors directly for their matrices, and some had them available to send to us (thank you!). It’s interesting that about a third of the “A” papers (24/76) do not have published character matrices. We may be able to reconstruct matrices from the text in some cases. We currently have 27 character matrices and 25 remain to be manually entered.

Annotating the skeletal phenotypes in these papers using EQ syntax and ontologies is our current challenge, along with merging old Phenote files into new Phenex format. We are taking a first-pass through the characters, initially coding the easy ones (e.g. Basibranchial 1 one present or absent) and submitting needed terms to the Teleost Anatomy Ontology (to see these terms and comment on them as proposed, please subscribe). We currently have 11 papers curated at this level; our goal is to do a first pass through most if not all of the A papers before our second data jamboree, where taxon experts will review and edit the data.

I want to thank our Deep-Fin sponsored Phenoscape intern this summer, Sonia Crichigno, who worked with our Ontology Curator Dr. Wasila Dahdul to enter taxon lists and character EQs. I particularly want to thank our other summer students Carin Rambow and Leah Mabee, who gathered pdfs, scanned and OCR’d documents, organized and updated the Google spreadsheet, typed in character matrices, and made initial taxon lists. I also want to thank Dr. Miles Coburn, a close colleague of mine and friend of all of us involved in Phenoscape. Miles was an expert on cypriniform fishes, who was reviewing and updating taxon lists and beginning character curation when he was killed in a bicycle accident on August 16th. We all miss him.

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).

We have three overall goals with the Data Jamboree. The first is to train fish morphologists outside of our project to understand how to use the tools (primarily Phenote) and ontologies to generate phenotype annotations compliant with the EQ approach. 

The second is to develop, review and where necessary refine best practices guidelines for annotation, to ensure that different morphologist generate the same, or at least semantically equivalent phenotype assertions from the same character descriptions.

The third goal is to generate actual data. Hence, after an initial training exercise, over the next two and a half days the morphologists and our curators will be going over a pre-selected set of publications and translate the character descriptions into EQ-compliant assertions, and the informaticists among us as well as our advisors will look over their shoulders to see what needs refinement.

• Museum collection code name completion when entering specimens for a taxon.
• Separate editable table for entering specimens for a taxon.
• Field for spatial ontology.
• Post-composition enabled for PATO fields.

The ontologies were deposited into the OBO versioning system already in November, but a database loading problem prevented their functioning in the BioPortal browser earlier.