Each of the people named below deserves special thanks for their contributions.
Victor McKusick, creator of Mendelian Inheritance in Man (MIM) and its later online version (OMIM, on which OMIA is modelled), provided moral support from the very first time the possibility of an animal equivalent of MIM was raised with Victor by Frank Nicholas at the International Congress of Genetics in Moscow in 1978. Jan Graham spent three years from 1980, chasing up old references and entering them into a bibliographic database entitled Mendelian Inheritance in Animals (MIA), constructed by Steve Brown on a University of Sydney mainframe computer, under the UNIX operating system. Steve worked wonders on the mainframe. Around 1990, the bibliographic information was moved to the SCIMATE bibliographic database on an IBM-compatible 286 desktop microcomputer. A year or so later, the bibliographic information was moved again to a powerful relational database called Advanced Revelation (ARev), first on the microcomputer and then onto Frank's laptop. Steve's ARev software was in regular use for more than 20 years.
From soon after its inception at the University of Sydney in 1991, the Australian National Genomic Information Service (ANGIS) became the obvious home for MIA and later its later online version, OMIA. Peter Reeves (a co-founder of ANGIS) and Alex Reisner (the first person in charge of day-to-day ANGIS management) provided much support and encouragement in the early 1990s. Paul le Tissier, a post-doc with Chris Moran from 1990-1993, contributed much enthusiasm and many ideas during the development of the ARev database, and beyond. Peter Reeves continued his support and encouragement until the closure of ANGIS in 2010.
By the mid-1990s, the very fruitful collaboration with ANGIS had reached the stage where it was feasible to consider launching an online version of MIA on an ANGIS server. In 1995, Carolyn Bucholtz, ANGIS’ programmer and database guru, took a flat file exported from ARev (via Steve Brown’s software) and worked her wonders in creating the original OMIA web page, populating it with the flat file behind the then OMIM BIRX search engine kindly provided by Dennis Benson and Randy Huntzinger from NCBI, with support from David Lipman. Victor McKusick solved a pivotal problem with permissions to cite references, enabling the web page to be made public on 26th May 1995. Its domain name was www.angis.su.oz.au/Databases/BIRX/omia/omia_form. By May 1997, the domain name had been abbreviated to the much more elegant omia.angis.org.au.
At the request of the USDA's National Agricultural Library (NAL) in Washington, OMIA was made available to the NAL, who packaged it into ACeDB software, linked it with the Agricola bibliographic database and with OMIM, and made it available (on 16th August, 1995) on the home page of USDA's Agricultural Genomic Information Server. Gail Juvik, Stephen M. Beckstrom-Sternberg and Jon T. Krainak were the enthusiastic drivers of this initiative, which continued until the NAL's genomics databases were transferred to Cornell University at the end of 1999. Maria Nemchuk continued the operation at Cornell, until it, too, was decommissioned in 2002.
David Lipman, from NCBI, and staff from Johns Hopkins University (in particular Joanna Amberger) enabled reciprocal linking of OMIM with OMIA, which came into operation on 16th October 1997.
Camson Huynh, from ANGIS, took over web responsibilities from Carolyn. Later, Dao Mai, also from ANGIS, wrote code for automatically replacing the ARev flat file. Carolyn's web site was in constant use for almost 10 years. Tim Littlejohn provided much enthusiastic support during his tenure as CEO of ANGIS from December 1995 until June 2001.
In 2002, Paul McGreevy, a colleague in the Faculty of Veterinary Science at the University of Sydney, organised an assessment exercise for first-year Veterinary Science students to prepare text entries for some of the clinical fields (in lay terms) that had laid blank for so long, in relation to inherited disorders of dogs. Because OMIA then still resided on a laptop, it was not possible to add the student's text to the OMIA fields. Instead, a separate database called Listing of Inherited Disorders in Animals (LIDA) was created by a team comprising Paul McGreevy, Federico Costa, Paul Della Torre, Peter Thomson and Frank. This database contained lists of breeds affected by each disorder, obtained from the web site of the Association of Veterinarians for Animal Rights. By 2005, the plan was for LIDA to concentrate on gathering prevalence data from veterinary practices. This became a reality with the launch of VetCompass in the UK (2007) and in Australia (2016).
Early in 2004, Mike Poidinger, then Head of ANGIS, generously took all the tables exported from the ARev database on Frank's laptop and placed them in a new MySQL database on an ANGIS server. He also picked up the PubMed URLs for thousands of references. Johann Lenffer took Mike's creation and, under the guidance of Mike and Shoba Ranganathan (Biotechnology Research Institute, Macquarie University), developed it into a database with an interactive web page that was ready for beta-testing. Late in 2004, Kao Castle took over from Johann, further developing the database and new web page.
Early in 2005, Matthew Mailman from the National Center for Biotechnology Information (NCBI) expressed interest in linking OMIA to a phenotype database under development at NCBI. This proved to be the beginning of a very fruitful collaboration, culminating in a mirror of OMIA being hosted at NCBI as an Entrez database. Matt deserves special thanks for all his efforts in bringing this development to fruition, as does Kao Castle for working closely with Matt, albeit across the Pacific Ocean.
In August 2005, the new OMIA database and website was further developed by Stefan Gregory, a programmer in ANGIS (and a guitarist in the rock band Faker 2004-2009!), with substantial inputs from Johann, who rejoined the team again after completing his honours research project, and from Arjun Rao, a medical practitioner who, in addition to providing several enhancements, put his clinical knowledge to very good use in mapping OMIA entries to the Mammalian Phenotype Ontology, and expanding the capacity of the Ontology.
With all the help outlined above, on 10th September 2005 we reached the stage where Carolyn's original web page could be retired, and the two new versions of OMIA - the new ANGIS interface and the NCBI Entrez mirror (OMIA@NCBI) - were launched. It was revolutionary to be able to add a reference or change some text, and immediately see those changes on the website!
Early in 2007, the master OMIA database was transferred to a new server funded through the SheepGenomics program by Meat and Livestock Australia (MLA) and Australian Wool Innovation (AWI). Oscar Luo (SheepGenomics) set up the server and transferred all the data and applications to it, with substantial and on-going help from Dao Mai (ANGIS). Jonathan Usmar (SheepGenomics) was responsible for maintenance of the site (in collaboration with Dao Mai), and for various enhancements, from then until the end of 2009.
In July 2007, Matt Mailman's direct involvement with OMIA ended when he moved from NCBI. It is a pleasure to record a very sincere thankyou to Matt for all his efforts in establishing OMIA@NCBI. His OMIA responsibilities were taken over by Donna Maglott, Mike Feolo and Rinat Bagoutdinov, all of whom immediately set about working with Oscar Luo to lay the groundwork for an automatic weekly update of OMIA@NCBI from the Sydney master database. In November 2007, Xuan Zhang became the person responsible for OMIA@NCBI. After various delays due to pressures of other commitments at the Sydney end, in February 2008 a very fruitful collaboration between Xuan and Jonathan Usmar came to fruition in the activation of an automatic weekly update of OMIA@NCBI from a dump of the entire OMIA database in Sydney.
In March 2010, consequent upon the decommissioning of the Sheepgenomics server, the master OMIA database was transferred to a virtual server hosted by Information and Communications Technology (ICT) at the University of Sydney. Under the very capable hands of Matthew Hobbs (a colleague within the Faculty of Veterinary Science), this task was achieved with input from Jonathan Usmar and ICT colleagues Stuart Johnston, Ivan Teliatnikov, Rowena Foss, Madeleine McCabe and Greg Rudd.
Commencing in August 2010, Matthew Hobbs began a major overhaul of the OMIA master database and development of a new website with improved curation tools, based on django, a high-level Python Web framework. On 10th August 2011, Matthew's new version of OMIA was launched.
From July until September 2011, a team assembled by Dr Vicki Meyers-Wallen (from the Baker Institute of Animal Health, College of Veterinary Medicine, Cornell University) greatly expanded 55 OMIA entries comprising 46 canine disorders and 9 feline disorders. Other members of the team were Martha MaloneyHuss, a veterinary student at Cornell, and the following colleagues from other institutions: Dr. Mark Haskins, University of Pennsylvania; Dr. John Fyfe, Michigan State University; Dr. Paula Henthorn, University of Pennsylvania; Dr. Margret Casal, University of Pennsylvania; Dr. Meg Sleeper, University of Pennsylvania. The contributions by each member of the team are gratefully acknowledged.
In February 2012, links from OMIM to OMIA were reinstituted with the new OMIM web resource, thanks to very fruitful interaction between François Schiettecatte (FS Consulting, LLC; consultant to OMIM) and Matthew Hobbs (OMIA). The links are automatically updated from the OMIA list of animal disorders and other traits for which there is strong evidence of human homology. The links are accessible from the Animal Models section of the Links tool on relevant OMIM pages. Thanks are also due to Joanna Amberger (Program Manager, OMIM) through whom this development was organised.
In June 2012, Matthew Hobbs created a "printing pipeline" for generating a hard-copy printed version of the entire contents of OMIA.
In January 2013, during the PAG XXI conference in San Diego, the OMIA Support Group was established. Thanks to Zhiliang Hu, with the support of Jim Reecy, the Support Group was given a home at https://www.animalgenome.org/community/omia-support/. Zhiliang also added an OMIA track to each of the genome browsers at https://animalgenome.org, providing links to OMIA from any gene in any relevant species in which a mutation is known to cause a specific phenotype.
In April 2013, OMIA data relating to every disorder/trait with a known causal/key mutation were incorporated into Ensembl (http://ensembl.org). From then until the present, every new Ensembl release contains updated OMIA information. Thanks to Fiona Cunningham, Andrew Yates, William McLaren and Laura Clark from EMBL-EBI, Hinxton, UK, for this important development.
Commencing in December 2013, Carrie Finno revised and updated the horse entries in the context of preparing a review of equine inherited disorders (Finno & Bannasch, 2014, Equine Vet J. 46:538-44).
On 16th April 2014, NCBI decommissioned their OMIA mirror, due to funding constraints. Frank Nicholas takes this opportunity to thank all the NCBI staff (and especially Xuan Zhang) who, since February 2008, have enabled the NCBI mirror to be maintained, and who have provided behind-the-scenes help in many ways.
In 2014 and 2015, Jim Reecy and Zhiliang Hu very generously led grant applications to the USDA for three major OMIA enhancements: ontologies, text mining and tables of likely causal variants. Unfortunately, each application was a near miss. But the momentum and the collaborative teams created via those grant applications continue to bear fruit, as described below.
On 13th April 2015, the domain name omia.org was purchased from a domain registrar for the princely sum of US$425. The domain name omia.angis.org.au was retired after 18 years of loyal service and was replaced by omia.org, which highlights the close relationship of OMIA with OMIM (omim.org).
In March 2016, Frank Nicholas became aware of PubTator, "a Web-based tool for accelerating manual literature curation . . . through the use of advanced text-mining techniques". One of PubTator's developers, Zhiyong Lu, from NCBI, kindly agreed to prepare a PubTator search that would capture PubMed references that involve (any human gene symbol OR any word in the OMIM "dictionary") AND any vertebrate animal species except humans, mice, rats and zebrafish. A weekly update of this search was inaugurated on 11 August 2016. Frank is very grateful to Zhiyong for all the effort he put into enabling OMIA searches to be conducted via PubTator, and to Chih-Hsuan Wei, the main developer of this exceedingly helpful tool.
From 2017, Ernie Bailey (University of Kentucky) has taught a course on OMIA, allocating each student to one or more equine OMIA entries in need of enhancement. These courses have generated many improvements to OMIA equine entries, with each student being acknowledged in the relevant entry.
Consequent upon an initial suggestion by Cali Willet (a colleague in the University of Sydney's Informatics Hub), an OMIA enhancement project was commenced on 20th July 2017 within the University's Centre for Translational Data Science and Sydney Informatics Hub. The project was conducted by Josh Stretton under the supervision of Jared Berghold and then Peter Thiem. The project involved incorporating existing information on likely causal variants into the OMIA db, displaying this information in a tabular, readily-downloadable format, and creating curation tools for incorporating information on new likely causal variants. The resultant new version of OMIA went public on 11 December 2017.
Thanks to the boundless support and strategic planning of Goncalo Borges from the University of Sydney's Information and Communications Technology (ICT, which has generously hosted OMIA since March 2010), and the subsequent amazing efforts of software engineer Di Lu (whose services were provided by the University of Sydney's Centre for Translational Data Science/Sydney Informatics Hub), working under the supervision of Peter Thiem and then Joel Nothman, an upgraded version of OMIA was launched on 14th November 2018. The new version of OMIA reflects a comprehensive upgrade of the computing infrastructure, including establishment of a secure https protocol devised by Goncalo and implemented by Di and Goncalo. It also includes a text-mining tool (developed and implemented by Di, making considerable use of NCBI’s PubTator) for curators that will greatly enhance the efficiency of curation.
Thanks are also due to software engineer Aaquib Ladiwala, supported by bequest funding to the Sydney School of Veterinary Science, who created several enhancements to OMIA that were included in the 14th November upgrade. Funding for Aaquib’s enhancements was kindly provided by the then Dean of the Sydney School of Veterinary Science, Rosanne Taylor. When Aaquib had to withdraw due to ill-health, his role was taken by Dhan Thapa Magar who, between December 2018 and May 2019, developed and launched several important enhancements including a new user-analytics package and a crowdfunding resource linked to the university's crowdfunding website. The enthusiastic encouragement of OMIA by Rosanne’s successor, Frazer Allan, is also greatly appreciated.
The OMIA crowdfunding appeal was launched on 18 March 2019. Special thanks are due to OMIM's Joanna Amberger, and to the following University of Sydney colleagues: Jude O'Hagan (Division of Alumni and Development), Claudia Zhang (Finance Manager), Isabella Andrews (manager of the University of Sydney’s crowdfunding platform), and Dhan Thapa Magar (software engineer). From October to December 2019, a portion of the funds raised from the crowdfunding appeal was devoted to the resolution of three emergencies by software engineer Hitesh Wagle. Thank you, Hitesh.
In September 2019, Darya Vanichkina became the leader of OMIA projects in the Sydney Informatics Hub. Darya is particularly thanked for her enthusiasm in leading the development of a proposal for a project to rationalize the submission of likely causal variants to the European Variation Archive (EVA), and the extraction by OMIA of relevant variant information from EVA. This project involves collaboration with Tosso Leeb, Cord Drögemüller and Vidhya Jagannathan (Institute of Genetics, University of Bern), Zhiliang Hu (National Animal Genome Research Program (Iowa State University), Thomas Keane and Baron Koylass (European Genome-phenome Archive and European Variation Archive, EBI). This project ran from November 2019 to 22 December 2021. Among other things, software engineer Marius Mather (working under Darya) created a set of tools that enable curators to create VCF files and metadata files that satisfy all of EVA's submission requirements. The task of actually gathering sufficient information on these variants to enable them to be submitted to EVA turned out to be very labour-intensive. Most of the labour was undertaken by Imke Tammen, Stephanie Shields, Katie Eager and Shernae Woolley, mainly on variants in cattle, sheep, goats and pigs. All this effort and Marius' tools enabled 504 variants to be submitted to EVA in October 2021. When EVA has completed processing the submission, 51% of OMIA variants will have an rsid, compared with 7% at the start of the project. This is a huge leap forward. In the first two months of 2022, Imke Tammen has led similar labour-intensive gathering of information on variants in dogs (with Tosso Leeb, Vidhya Jagannathan, and with UCSC Genome Browser's Bob Kuhn and Mateo Etcheveste) and in horses (with Ernie Bailey and an OMIA class devoted to this task). When these dog and horse variants have been processed by EVA, the proportion of OMIA variants with rsids should be substantially greater than 51%.
Darya has also been very helpful in enabling several minor OMIA tasks to be done, not least of which is the downloading of the entire contents of OMIA on 26th May 2020, using Matthew Hobbs' 2012 "pipeline", for publication as a book to mark OMIA’s 25th birthday.
Over the years many colleagues have provided support, encouragement and enhancements (in addition to their own discoveries) to particular OMIA entries: Imke Tammen, Tosso Leeb, Cord Drögemüller, Leif Andersson, Ernie Bailey, Claire Wade, Bianca Hasse, Hamutal Mazrier, Cali Willet, Tracy Chew, Bobbie Cansdale, Brandon Velie, Yizhou Chen, Reza Shariflou, and Bethany Wilson. In recent years, some of these colleagues have joined Frank’s tentative venture into online curation tutorials.
In 2020, Tianna Grant reviewed and updated OMIA entries relating to marine mammals as part of her DVM3 research project. Since March 2020, David Silversides, from the Laboratory of Veterinary Genetics, Faculty of Veterinary Medicine, University of Montreal, has been a very diligent spotter of missing references and/or inconsistent entries. His very useful suggestions are much appreciated.
In 2021, Rachel Natsume reviewed and updated OMIA entries relating to feline kidney disease as part of her DVM3 research project. Since 2021, PhD candidate Leah Manning is contributing to entries relating to neurological conditions in ruminants.
From early in 2021, OMIA has greatly benefited from work performed by staff at the Sydney Informatics Hub (SIH), funded from a bequest to the Sydney School of Veterinary Science that is enabling the creation of the Anstee Hub for Inherited Diseases of Animals (AHIDA). As a key resource for AHIDA, OMIA has been allocated some funding from the AHIDA bequest budget. Staff of the SIH, including Marius Mather, Elevn Li and Joel Nothman, upgraded the software infrastructure for OMIA, to enable its further development, while also resolving some painfully slow site performance and other issues. They have also added new capabilities to OMIA to modernise its knowledge and interoperation with other resources, including adding a Source of Variant field, distinguishing gene and trait MIM numbers, and laying the foundations for linking OMIA data to ontologies. At the same time, Darya Vanichkina and Marius Mather have worked on consolidating OMIA's genetic variant data in order to integrate it with EVA resources.
In 2022, Hannah Edgell reviewed and updated OMIA entries relating to CRISPR-Cas9 genome editing in sheep and Natalia Ramos Reyee reviewed and updated entries relating to the genus Panthera, as part of their DVM3 research projects. DVM students in VETS6303 Small Animal Practice A contributed to a review of cat and dog entries in OMIA with a focus on information relating to clinical findings and pathology.
On 8 July 2022, a set of commentaries on historic papers, called Pioneers of Mendelian Inheritance in Animals, was launched under a new PMIA tab on the OMIA home page, in the lead-up to the bicentenary of Mendel's birth on 22 July 2022. The enhancement that enabled this to happen was entirely the work of software engineer Marius Mather, from the University of Sydney's Sydney Informatics Hub. The work was funded from the Ronald Bruce Anstee bequest to the Sydney School of Veterinary Science, via funding for the Anstee Hub for Inherited Diseases in Animals (AHIDA).
In 2023, DVM students in VETS6303 Small Animal Practice A contributed to a review of cat and dog entries in OMIA with a focus on information relating to breeds, synonyms and clinical findings and pathology.
Vertebrate Breed Ontology
By late 2017, it had become evident that the home-grown breed list in OMIA needed to be replaced by a computable standardised set of breed names, including all synonyms. Late in 2020, as the AHIDA proposal was being put together, Frank Nicholas contacted the following US-based colleagues with whom he had had some previous interaction to do with ontologies: Melissa Haendel (Translational and Integrative Sciences Laboratory (TISLab), then at the Oregon Health & Science University; now at the Anschutz Medical Campus of the University of Colorado), Chris Mungall (Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory), Peter Robinson (The Jackson Laboratory for Genomic Medicine), and Zhiliang Hu and Jim Reecy (Department of Animal Science, Iowa State University; developers of (among many other resources) the Livestock Breed Ontology (LBO) and hosts of https://animalgenome.org). All of these people generously agreed to be named as international collaborators on the AHIDA project. By early 2021, by which time funding from the AHIDA project had become available, it became possible to begin planning a project to create a standardised set of breed names in the form of an ontology, to be used in OMIA and AHIDA, as a trial run for the more challenging task of creating a phene ontology for OMIA and AHIDA. To this end, an international collaborative team was established largely from within the Monarch Initiative (https://monarchinitiative.org/), led by Melissa Haendel. Other members comprised Chris Mungall, Nicole Vasilevsky (TISLab), Zhiliang Hu, Jim Reecy (joined by Cari Park, also from the Department of Animal Science, Iowa State University), Gregoire Leroy and Roswitha Baumung (Domestic Animal Diversity Information System (DADIS), FAO, Rome), and Nico Matentzoglu (Semanticly, Athens, Greece). University of Sydney members of the team were Frank Nicholas, Imke Tammen and (from the Sydney Informatics Hub) Marius Mather, resourced via AHIDA funding. Sabrino Toro (TISLab) joined the team in June 2021. Unfortunately, the overlap between LBO and the OMIA home-grown breed list was less than expected (due to the very different areas covered by OMIA and animalgenome.org). Consequently, it was decided to use the FAO’s DADIS breed list as the basis for what became known as the Vertebrate Breed Ontology (VBO). With Sabrina working at the VBO coalface, ably and generously supported by the rest of the team, the first version of VBO (incorporating around 8,800 breed names (with known synonyms) across 37 livestock species, as compiled by FAO from information provided by a national breed coordinator from each of 182 countries) was released on the Monarch Initiative GitHub website (https://github.com/monarch-initiative/vertebrate-breed-ontology) on 6 May 2022. By that time, Melissa Haendel had generously resourced a postdoctoral position to work with Sabrina on the VBO, enabling Katie Mullen to join the TISLab team in Colorado in May 2022. Halie Rando also joined the team. The first version of VBO was accepted into the OBO Foundry (https://obofoundry.org/ontology/vbo.html) on 5 September 2022. A second version of VBO, incorporating cat breeds gleaned primarily by Katie from major international and national resources, was released on GitHub and OBO Foundry on 22 September 2022, and the next day was also released on two Ontology Lookup Services (OLS): https://www.ebi.ac.uk/ols/ontologies/vbo and https://ontobee.org/ontology/vbo. The OLS release was particularly important because it is the resource from which OMIA and AHIDA will interrogate the VBO. Importantly, VBO is freely accessible from either OLS for use by any organisation or resource that wishes to use it. At present, VBO is far from complete and should be regarded as being in the beta-testing phase. Feedback to [email protected] is welcomed.
Grateful thanks are extended to:
- H.G. Slater Foundation, for a grant of A$2000 in 1979, that assisted in the initial establishment of the mainframe database.
- (Australian) Commonwealth Special Research Grant, for a grant of A$46,386 in 1980-1982, that enabled Jan Graham to enter references into the mainframe database.
- International Livestock Centre for Africa (ILCA), for a grant of A$9,423 in 1983, that helped to fund the development of the mainframe database.
- Food and Agriculture Organization (FAO) of the United Nations, for a grant of A$8,990 in 1993, that helped fund the initial development of OMIA as a web resource.
- Friends of the [Queensland] Veterinary School Inc, for a donation of A$1,483.64 (courtesy of Professor Keith Hughes) in 1996, for the development of OMIA.
- American Humane Association, for funding Martha MaloneyHuss to upgrade many canine and feline entries, under the supervision of Dr Vicki Meyers-Wallen (College of Veterinary Medicine, Cornell University), in the northern summer of 2011.
- University of Sydney, for providing the services of software engineer Josh Stretton (via the University's Centre for Translation Data Science and Sydney Informatics Hub) for two days per week from August to December 2017. Josh's efforts resulted in the launch of a new version of OMIA on 11 December 2017, presenting information on likely causal variants in a standard sortable and downloadable format.
- University of Sydney, for providing the services of software engineer Di Lu (via the University's Centre for Translation Data Science and Sydney Informatics Hub). Di's efforts resulted in the launch of a new version of OMIA on 14th November 2018, incorporating a substantial infrastructure upgrade and a text-mining strategy that has greatly increased the efficiency of finding and incorporating new relevant information into OMIA.
- The Sydney School of Veterinary Science, for providing $5000 of bequest funding that enabled software engineer Aaquib Ladiwala to develop several enhancements that were included in the 14th November upgrade. This funding was initially provided by former Dean Professor Rosanne Taylor, and was subsequently endorsed by her successor Professor Frazer Allan. Due to illness, Aaquib was not able to complete all the enhancements on which he was working. Dhan Thapa Magar ably took over Aaquib's role, completing several major enhancements.
- The numerous people who have donated to OMIA's crowdfunding appeal that was launched on 19th March 2019. They are listed under the Donate tab accessible from the OMIA home page.
- Since 2021, ongoing maintenance and improvements from software engineers from the Sydney Informatics Hub have been possible due to the generous funding from the Ronald Bruce Anstee bequest to the Sydney School of Veterinary Science for the Anstee Hub for Inherited Diseases in Animals (AHIDA).