Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier
Thessen, Anne E
Cole, Heather A
Chong, Steven S
MetadataShow full item record
CitationEndara L, Thessen A, Cole H, Walls R, Gkoutos G, Cao Y, Chong S, Cui H (2018) Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier. Biodiversity Data Journal 6: e29232. https://doi.org/10.3897/BDJ.6.e29232
JournalBIODIVERSITY DATA JOURNAL
Rights© Endara L et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0).
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at email@example.com.
AbstractBackground: When phenotypic characters are described in the literature, they may be constrained or clarified with additional information such as the location or degree of expression, these terms are called "modifiers". With effort underway to convert narrative character descriptions to computable data, ontologies for such modifiers are needed. Such ontologies can also be used to guide term usage in future publications. Spatial and method modifiers are the subjects of ontologies that already have been developed or are under development. In this work, frequency (e.g., rarely, usually), certainty (e.g., probably, definitely), degree (e.g., slightly, extremely), and coverage modifiers (e.g., sparsely, entirely) are collected, reviewed, and used to create two modifier ontologies with different design considerations. The basic goal is to express the sequential relationships within a type of modifiers, for example, usually is more frequent than rarely, in order to allow data annotated with ontology terms to be classified accordingly. Method: Two designs are proposed for the ontology, both using the list pattern: a closed ordered list (i.e., five-bin design) and an open ordered list design. The five-bin design puts the modifier terms into a set of 5 fixed bins with interval object properties, for example, one_level_more/less_frequently_than, where new terms can only be added as synonyms to existing classes. The open list approach starts with 5 bins, but supports the extensibility of the list via ordinal properties, for example, more/less_frequently_than, allowing new terms to be inserted as a new class anywhere in the list. The consequences of the different design decisions are discussed in the paper. CharaParser was used to extract modifiers from plant, ant, and other taxonomic descriptions. After a manual screening, 130 modifier words were selected as the candidate terms for the modifier ontologies. Four curators/experts (three biologists and one information scientist specialized in biosemantics) reviewed and categorized the terms into 20 bins using the Ontology Term Organizer (OTO) (http://biosemantics.arizona.edu/OTO). Inter-curator variations were reviewed and expressed in the final ontologies. Results: Frequency, certainty, degree, and coverage terms with complete agreement among all curators were used as class labels or exact synonyms. Terms with different interpretations were either excluded or included using "broader synonym" or "not recommended" annotation properties. These annotations explicitly allow for the user to be aware of the semantic ambiguity associated with the terms and whether they should be used with caution or avoided. Expert categorization results showed that 16 out of 20 bins contained terms with full agreements, suggesting differentiating the modifiers into 5 levels/bins balances the need to differentiate modifiers and the need for the ontology to reflect user consensus. Two ontologies, developed using the Protege ontology editor, are made available as OWL files and can be downloaded from https://github.com/biosemantics/ontologies. Contribution: We built the first two modifier ontologies following a consensus-based approach with terms commonly used in taxonomic literature. The five-bin ontology has been used in the Explorer of Taxon Concepts web toolkit to compute the similarity between characters extracted from literature to facilitate taxon concepts alignments. The two ontologies will also be used in an ontology-informed authoring tool for taxonomists to facilitate consistency in modifier term usage.
VersionFinal published version
SponsorsUS National Science Foundation [DBI-1661485, IOS:1340112, DBI-1147266, DEB-1541506]; H2020-EINFRA 
- OTO: Ontology Term Organizer.
- Authors: Huang F, Macklin JA, Cui H, Cole HA, Endara L
- Issue date: 2015 Feb 15
- Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.
- Authors: Dahdul W, Manda P, Cui H, Balhoff JP, Dececchi TA, Ibrahim N, Lapp H, Vision T, Mabee PM
- Issue date: 2018 Jan 1
- MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.
- Authors: Blank CE, Cui H, Moore LR, Walls RL
- Issue date: 2016
- Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.
- Authors: Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, Kothari C, Lapp H, Lundberg JG, Midford PE, Vision TJ, Westerfield M, Mabee PM
- Issue date: 2010 May 20
- The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions.
- Authors: Wirkner CS, Göpel T, Runge J, Keiler J, Klussmann-Fricke BJ, Huckstorf K, Scholz S, Mikó I, J Yoder M, Richter S
- Issue date: 2017 Sep 1
Showing items related by title, author, creator and subject.
Effects of orientation and mobility of surface modifiers on the selectivity and efficiency of chemical interactions at selected chemically modified surfaces.Burke, M.F.; Palmer, Christopher Paul.; Denton, M.B.; Pemberton, Jeanne E.; Barfield, M.; Vemulapalli, Krishna G. (The University of Arizona., 1991)Several surfaces chemically modified with a variety of surface modifiers have been studied using chromatographic, nuclear magnetic resonance, and computational techniques. The goal was to determine the effect of modifier structure on the solvation, selectivity, and efficiency of chemical interactions occurring at chemically modified surfaces. Oleyldimethylchlorosilane has been synthesized and bonded to silica to determine the effect of a conformational change at the center of the chain on the behavior of the entire surface. It has been shown with these studies that the configuration of the modifier plays an important role in determining the selectivity of chemical interactions at modified surfaces. By comparison with phospholipid bilayers, of the structure, solvation and dynamics of alkylmodified silicas has been achieved. Octyldimethylsilyl- and octadecyldimethylsilyl-modified silicas have been further reacted with t-butyltrichlorosilane, t-butyldimethylchlorosilane and trimethylchlorosilane to determine both the utility of t-butyltrichlorosilane as an end-capping reagent and the extent to which solvation of the near-surface region affects the performance of these surfaces. It was shown that the orientation and solvation of modifiers at the near surface has a profound effect on the selectivity and efficiency of chemical interactions at the surface. Sepharose gels modified with iminodiacetic acid have been studied by titrimetric and spectroscopic means. A model compound has been synthesized and characterized in solution. The results have led to a better understanding of the behavior of chelating agents at sepharose surfaces and the effects of immobilization on the behavior of ligands at a surface. Finally, quartz crystalline microbalances modified with physisorbed polymer layers have been studied by correspondence analysis. In this case, it has been shown that the polymer backbone of the modifying agent plays an important role in determining the selectivity of the modified surfaces. Together these studies have led to a more complete understanding of the effects of the structure and solvation of modified surfaces on the selectivity and efficiency of chemical interactions occurring at those surfaces. These observations apply to interactions occurring at chromatographic stationary phases and to interactions at chemically modified surfaces in general.
Modified Cocomo Model For Maintenance cost Estimation of Real Time System SoftwareChakraverti, Sugandha; Kumar, Sheo; Agarwal, S. C.; Chakraverti, Ashish Kumar; Department of CSE, MBU Solan, HP-173229, India; Department of Mathematics, KCCEC Greater Noida UP-201308, India; Department of CSE, BBDIT Ghaziabad, UP-201002, India (IJCSN, 2012-02-15)Accurate cost estimation of software projects is one of the most desired capabilities in software development Process. Accurate cost estimates not only help the customer make successful investments but also assist the software project manager in coming up with appropriate plans for the project and making reasonable decisions during the project execution. Although there have been reports that software maintenance accounts for the majority of the software total cost, the software estimation research has focused considerably on new development and much less on maintenance. Now if we talk about real time software system(RTSS) development cost estimation and maintenance cost estimation is not much differ from simple software but some critical factor are considered for RTSS development and maintenance like response time of software for input and processing time to give correct output. As like simple software maintenance cost estimation existing models (i.e. Modified COCOMO-II) can be used but after inclusion of some critical parameters related to RTSS. A Hypothetical Expert input and an industry data set of eighty completed software maintenance projects were used to build the model for RTSS maintenance cost. The full model, which was derived through the Bayesian analysis, yields effort estimates within 30% of the actual 51% of the time,outperforming the original COCOMO II model when it was used to estimate theseprojects by 34%. Further performance improvement was obtained when calibrating the full model to each individual program, generating effort estimates within 30% of the actual 80% of the time.
Safety assessment of genetically modified crops for yield increase and resistance to both biotic and abiotic stresses and their impact on human and environmentAskari-Khorasgani, Omid; Pessarakli, Mohammad; Univ Arizona, Sch Plant Sci (MedCrave, 2018-03-06)Biotechnology has now accelerated the breeding evolution of agricultural products to obtain stress-tolerant crops with improved productivity to meet the increasing global demand which is in direct correlation with demographic trends. Nutritional quality, food allergies, toxicity effects, and unwanted resistance and alternations in gene sequences are the main concerns of genetically engineered products. Despite the numerous and overall benefits of genetically engineered crops, the questions raised by unwanted and unpredictable consequences about their safety concerns that may harm human, animal, and/or the ecosystem health require a long-term and a case-by-case transparent assessments before releasing the biotech crops into the food chain.