Merging the NBO and ABO Ontologies for Behavior · Merging the NBO and ABO Ontologies for Behavior...
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Merging the NBO and ABO Ontologies for Behavior References Deans, A.R., et al.,. 2015. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. doi:10.1371/journal.pbio.1002033 Mabee, P., Balhoff, J. P., Dahdul, W. M., Lapp, H., Midford, P. E., Vision, T. J. and Westerfield, M. (2012), 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. Journal of Applied Ichthyology, 28: 300–305. doi: 10.1111/j.1439-0426.2012.01985.x Martins, E. P. 2004. “EthoSource: Storing, Sharing, and Combining Behavioral Data.” BioScience 54 (10): 886. doi:10.1641/0006-3568(2004)054[0886:ESSACB]2.0.CO;2 Acknowledgments The workshops described here were supported by the Phenotype Ontology Research Coordination Network; NSF-DEB-0956049; http://www.phenotypercn.org/ and directly by the NSF (NSF-IOS-1439561) and the Animal Behavior Society. The opinions expressed here do not represent those of the Phenotype Ontology RCN, the Animal Behavior Society or the NSF. We would also like to thank workshop attendees , Katja Schultz (Encyclopedia of Life), Elissa Chesler (Jackson Laboratory), George Gkoutos (University of Birmingham), David Osumi-Sutherland(European Bioinformatics Institute), Melissa Haendel (remote; Oregon Health and Science University) Reid Rumelt (Cornell University/ Macaulay Library) Why Ontologies (Vocabularies) Matter Ontologies, controlled vocabularies that capture formal relationships among terms, are an increasingly popular tool for representing medical, and more recently, comparative biological knowledge (Mabee et al. 2012, Deans et al. 2015). Ontologies are commonly used in the annotation of data, particularly media and textual descriptions, and also in ‘semantic’ queries of databases. Most of the interest in ontologies has been at the cellular or anatomical level. However, several research communities have been developing ontologies to describe behavior in humans, model and non-model organisms. This poster describes recent efforts to merge two of these vocabularies. NeuroBehavior Ontology (NBO) NBO had its roots in a phenotype vocabulary supporting the EUMORPHIA project (http:// www.europhenome.org/). Behavior terms were initially included in the Gene Ontology, but also included in several phenotype ontologies, (e.g., Mammalian Phenotype ontology, Human Phenotype Ontology) to enable encoding of behavior phenotypes. The NBO was developed to combine and link behavior phenotypes and processes. Animal Behavior Ontology (ABO) Midford, P. E. 1 , Clark, A. B. 2 , Margulis, S. W. 3 , Parr, C. S. 4 1 Unaffiliated, Richmond VA, 2 University at Binghamton, Binghamton NY, 3 Canisius College, Buffalo NY, 4 US Department of Agriculture ARS, Beltsville MD Workshops Phenotype RCN Meeting (Durham 2013) The Phenotype Ontologies RCN was funded to develop applications of ontologies to the description of phenotypes. They met annually from 2010 to 2014. At the 2013 meeting in Durham, NC, the Behavior Breakout group discussed the existence of multiple behavioral ontologies, including the gaps in existing ontologies that preclude their widespread use in behavioral ecology and other sub-disciplines in animal behavior. The group felt it could be possible to merge two existing behavioral ontologies -- the NBO, developed to serve studies of animal models of human behavioral dysfunction, and the ABO, developed to serve the field of comparative animal behavior, including behavioral ecology and other sub-disciplines. If successful, the merger would facilitate the broader integration of behavioral studies, but it would also need to continue to serve the specialized needs of subfields. In late summer 2014, the authors (who were all present at the Durham meeting) were funded to hold two workshops to accomplish these goals. Animal Behavior Society workshop (Princeton 2014) Our first workshop, in August 2014 at Princeton University, convened over a dozen animal behaviorists with a broad range of expertise in comparative behavior to develop specific recommendations on how to integrate the basic terms and concepts of the two ontologies. Key outcomes included a list of proposed changes in parent-child relations in the NBO to emphasize function, and ABO term definition improvements that together could serve as the basis of integrating the two ontologies. Ontology Merging Workshop (Washington 2015) With our NSF funding and additional funding from the Phenotype RCN, we held a second workshop at the Smithsonian’s National Museum of Natural History, Washington, DC, on October 24-25, 2015. Its specific goal was to start the process of merging the ABO and the NBO based on the first workshop’s recommendations. Following a review of the histories of NBO and ABO, we spent the remainder of the workshop working to establish whether ABO ‘operational’ terms could be merged into NBO process terms. The discussion ended at the question of whether process terms ought to be in NBO at all, rather than added to the Gene Ontologies Biological Process branch. Progress since the merging workshop (Dec 2015) We made significant progress by the conclusion of the second workshop, but also recognized that we still had much work to do before completing a merger of the two ontologies. Since the second workshop, we have an ongoing effort to: (1) Continue refinement of ABO definitions (2) Identify synonymies between ABO terms and terms in NBO and Gene Ontology (3) Identify gaps that prevent the obvious addition of ABO terms into NBO; and (4) Identify any remaining technical issues (e.g., hierarchy problems, NBO identifier assignment) During a number of follow-up conferences calls, we succeeded in identifying several fundamental differences in the ways that the behavioral ecology and the model organism communities view and interpret the higher-order organization of the ontologies. For example, the broadest characteristics in NBO are “behavioral processes” and “behavioral phenotypes”, while in ABO they are “behavioral acts” and “behavioral functions”. “Acts” and “Processes” are largely comparable, but “phenotypes” are characteristics of NBO processes, whereas “functions” are the presumed Tinbergien adaptive interpretations of observed behavior. As the merger progresses, we envision adding a third branch to the NBO to capture the ABO “functional” behaviors, while integrating the ABO “acts” into NBO “processes”. Top of NBO class hierarchy Top of ABO class hierarchy ABO was originally proposed as a vocabulary component of the Ethosource repository of behavior data. Mapping between subsets of terms in NBO and ABO derived from products of 2014 Princeton Workshop. ABO was one of the first accomplishments of the EthoSource project (Martins 2004), begun with an NSF-sponsored workshop in 2000 with the goal of developing integrated online resources for the discipline of Animal Behavior. Two additional workshops followed in 2004-2005, at which an international group of animal behaviorists developed a basic metadata standard for the discipline, the ABO. The ABO includes hierarchies for behavior acts and behavior functions. The primary use of the ABO subsequent to 2005 was indexing an online ethogram repository, EthoSearch.org.
Transcript of Merging the NBO and ABO Ontologies for Behavior · Merging the NBO and ABO Ontologies for Behavior...
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Merging the NBO and ABO Ontologies for Behavior
References Deans, A.R., et al.,. 2015. Finding Our Way through Phenotypes. PLoS Biol, 13(1), e1002033. doi:10.1371/journal.pbio.1002033 Mabee, P., Balhoff, J. P., Dahdul, W. M., Lapp, H., Midford, P. E., Vision, T. J. and Westerfield, M. (2012), 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. Journal of Applied Ichthyology, 28: 300–305. doi: 10.1111/j.1439-0426.2012.01985.x Martins, E. P. 2004. “EthoSource: Storing, Sharing, and Combining Behavioral Data.” BioScience 54 (10): 886. doi:10.1641/0006-3568(2004)054[0886:ESSACB]2.0.CO;2
AcknowledgmentsThe workshops described here were supported by the Phenotype Ontology Research Coordination Network; NSF-DEB-0956049; http://www.phenotypercn.org/ and directly by the NSF (NSF-IOS-1439561) and the Animal Behavior Society. The opinions expressed here do not represent those of the Phenotype Ontology RCN, the Animal Behavior Society or the NSF. We would also like to thank workshop attendees , Katja Schultz (Encyclopedia of Life), Elissa Chesler (Jackson Laboratory), George Gkoutos (University of Birmingham), David Osumi-Sutherland(European Bioinformatics Institute), Melissa Haendel (remote; Oregon Health and Science University) Reid Rumelt (Cornell University/Macaulay Library)
Why Ontologies (Vocabularies) Matter
Ontologies, controlled vocabularies that capture formal relationships among terms, are an increasingly popular tool for representing medical, and more recently, comparative biological knowledge (Mabee et al. 2012, Deans et al. 2015). Ontologies are commonly used in the annotation of data, particularly media and textual descriptions, and also in ‘semantic’ queries of databases. Most of the interest in ontologies has been at the cellular or anatomical level. However, several research communities have been developing ontologies to describe behavior in humans, model and non-model organisms. This poster describes recent efforts to merge two of these vocabularies.
NeuroBehavior Ontology (NBO)
NBO had its roots in a phenotype vocabulary supporting the EUMORPHIA project (http://www.europhenome.org/). Behavior terms were initially included in the Gene Ontology, but also included in several phenotype ontologies, (e.g., Mammalian Phenotype ontology, Human Phenotype Ontology) to enable encoding of behavior phenotypes. The NBO was developed to combine and link behavior phenotypes and processes.
Animal Behavior Ontology (ABO)
Midford, P. E.1, Clark, A. B.2, Margulis, S. W.3, Parr, C. S.4
1Unaffiliated, Richmond VA, 2University at Binghamton, Binghamton NY, 3Canisius College, Buffalo NY, 4US Department of Agriculture ARS, Beltsville MD
Workshops Phenotype RCN Meeting (Durham 2013) The Phenotype Ontologies RCN was funded to develop applications of ontologies to the description of phenotypes. They met annually from 2010 to 2014. At the 2013 meeting in Durham, NC, the Behavior Breakout group discussed the existence of multiple behavioral ontologies, including the gaps in existing ontologies that preclude their widespread use in behavioral ecology and other sub-disciplines in animal behavior. The group felt it could be possible to merge two existing behavioral ontologies -- the NBO, developed to serve studies of animal models of human behavioral dysfunction, and the ABO, developed to serve the field of comparative animal behavior, including behavioral ecology and other sub-disciplines. If successful, the merger would facilitate the broader integration of behavioral studies, but it would also need to continue to serve the specialized needs of subfields. In late summer 2014, the authors (who were all present at the Durham meeting) were funded to hold two workshops to accomplish these goals. Animal Behavior Society workshop (Princeton 2014) Our first workshop, in August 2014 at Princeton University, convened over a dozen animal behaviorists with a broad range of expertise in comparative behavior to develop specific recommendations on how to integrate the basic terms and concepts of the two ontologies. Key outcomes included a list of proposed changes in parent-child relations in the NBO to emphasize function, and ABO term definition improvements that together could serve as the basis of integrating the two ontologies. Ontology Merging Workshop (Washington 2015) With our NSF funding and additional funding from the Phenotype RCN, we held a second workshop at the Smithsonian’s National Museum of Natural History, Washington, DC, on October 24-25, 2015. Its specific goal was to start the process of merging the ABO and the NBO based on the first workshop’s recommendations. Following a review of the histories of NBO and ABO, we spent the remainder of the workshop working to establish whether ABO ‘operational’ terms could be merged into NBO process terms. The discussion ended at the question of whether process terms ought to be in NBO at all, rather than added to the Gene Ontologies Biological Process branch. Progress since the merging workshop (Dec 2015) We made significant progress by the conclusion of the second workshop, but also recognized that we still had much work to do before completing a merger of the two ontologies. Since the second workshop, we have an ongoing effort to: (1) Continue refinement of ABO definitions (2) Identify synonymies between ABO terms and terms in NBO and Gene Ontology (3) Identify gaps that prevent the obvious addition of ABO terms into NBO; and (4) Identify any remaining technical issues (e.g., hierarchy problems, NBO identifier assignment) During a number of follow-up conferences calls, we succeeded in identifying several fundamental differences in the ways that the behavioral ecology and the model organism communities view and interpret the higher-order organization of the ontologies. For example, the broadest characteristics in NBO are “behavioral processes” and “behavioral phenotypes”, while in ABO they are “behavioral acts” and “behavioral functions”. “Acts” and “Processes” are largely comparable, but “phenotypes” are characteristics of NBO processes, whereas “functions” are the presumed Tinbergien adaptive interpretations of observed behavior. As the merger progresses, we envision adding a third branch to the NBO to capture the ABO “functional” behaviors, while integrating the ABO “acts” into NBO “processes”.
Top of NBO class hierarchy
Top of ABO class hierarchy
ABO was originally proposed as a vocabulary component of the Ethosource repository of behavior data.
Mapping between subsets of terms in NBO and ABO derived from products of 2014 Princeton Workshop.
ABO was one of the first accomplishments of the EthoSource project (Martins 2004), begun with an NSF-sponsored workshop in 2000 with the goal of developing integrated online resources for the discipline of Animal Behavior. Two additional workshops followed in 2004-2005, at which an international group of animal behaviorists developed a basic metadata standard for the discipline, the ABO. The ABO includes hierarchies for behavior acts and behavior functions. The primary use of the ABO subsequent to 2005 was indexing an online ethogram repository, EthoSearch.org.
