scholarly journals A Logical Model of Homology for Comparative Biology

2019 ◽  
Vol 69 (2) ◽  
pp. 345-362
Author(s):  
Paula M Mabee ◽  
James P Balhoff ◽  
Wasila M Dahdul ◽  
Hilmar Lapp ◽  
Christopher J Mungall ◽  
...  
Keyword(s):  
Comparative Anatomy ◽  
Homology Model ◽  
Comparative Biology ◽  
Search Term ◽  
Morphology Evolution ◽  
Query Term ◽  
Anatomical Structures ◽  
Serial Homology ◽  
Homology Relationship ◽  
Computational Reasoning

Abstract There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. [Homology; ontology; anatomy; morphology; evolution; knowledgebase; phenoscape.]

scholarly journals A logical model of homology for comparative biology

2019 ◽  
Author(s):  
Paula M. Mabee ◽  
James P. Balhoff ◽  
Wasila M. Dahdul ◽  
Hilmar Lapp ◽  
Christopher J. Mungall ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Comparative Anatomy ◽  
Homology Model ◽  
Comparative Biology ◽  
Search Term ◽  
Common Ancestry ◽  
Anatomical Structures ◽  
Serial Homology ◽  
Growing Body ◽  
Computational Reasoning

AbstractThere is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for vertebrate fins and limbs from the Phenoscape Knowledgebase (KB). Using six competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms Homology Model (REA) and the Ancestral Value Axioms Homology Model (AVA). Both models returned the user-expected results for all but one historical homology query and all serial homology queries. Additionally, for each competency question, the AVA model returns the search term and any subtypes. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery.

L'OMOLOGIA RIVISITATA

Nuncius ◽  
2003 ◽  
Vol 18 (1) ◽  
pp. 167-200
Author(s):  
ALESSANDRO MINELLI
Keyword(s):  
Developmental Biology ◽  
Hox Genes ◽  
Expression Patterns ◽  
Comparative Morphology ◽  
Evolutionary Developmental Biology ◽  
Developmental Pathways ◽  
Comparative Biology ◽  
Serial Homology ◽  
Near Future ◽  
Shaky Ground

Abstracttitle SUMMARY /title Many different and even contrasting notions of homology have been proposed over two centuries of comparative biology, beginning with the initial reference to idealised archetypes, down to the current concepts based on derivation from a common ancestor, or on shared developmental pathways or genetic (more extensively, informational) background. Select anatomical features such as the patterns of innervation, or the expression patterns of genes putatively involved in key developmental events, e.g. the Hox genes, have been repeatedly suggested as the most reliable cues to homology. This confidence, however, rests on shaky ground and results are never certain. Recent work in comparative morphology and evolutionary developmental biology increasingly suggests the need to abandon the traditional all-or-nothing notion of homology, in favour of a more flexible, factorial or combinatorial approach. In this way it will be possible to accommodate within one broad comparative view, respectful of phylogeny and developmental biology alike, many disparate notions such as positional and special homology, serial homology and temporal serial homology. All statements of homology, however, will thus require adequate qualification of the context specifically taken in consideration and the criteria used to address the comparison. It remains to be seen, in the near future, how far the old concept of homology, now under the burden of so many and so different notions, will still be of use to comparative biology.

scholarly journals Comparative anatomy of the thigh nerves of Cebus libidinosus (Rylands et al., 2000)

2011 ◽  
Vol 31 (3) ◽  
pp. 261-266 ◽  
Author(s):  
R.A.G.M.F. Aversi-Ferreira ◽  
K.A. Marin ◽  
F.O. Carneiro e Silva ◽  
T.A. Aversi-Ferreira
Keyword(s):  
Scientific Literature ◽  
Comparative Anatomy ◽  
Detailed Knowledge ◽  
Anatomical Structures ◽  
Important Group ◽  
Medical Clinics ◽  
Veterinary Importance ◽  
Pelvic Limb ◽  
Sciatic Nerves ◽  
Cebus Libidinosus

Non-human primates have constituted an important group among animals subjected to various studies. Ethological, evolutionary and paleontological studies have revealed changes in anatomical structures linked to the evolution of primates, considered in studies on the comparative anatomy between Cebus libidinosus and other neotropical monkeys or those from the Old World, and the detailed knowledge on their anatomy may represent an important factor for their preservation and protection when the animals are brought to veterinary clinics after accidents or illnesses. In terms of veterinary importance, sometimes these animals arrive in the veterinary medical clinics after accidents, needing surgery or clinical treatment, but the little data available on anatomy has impaired the correct proceedings. The main justification for studies on C. libidinosus, is due to little information about the anatomy related to C. libidinosus in Brazilian and worldwide scientific literature. In this study, the distribution, enervation and path of the femoral and sciatic nerves of the pelvic limb (thigh) of C. libidinosus were studied and these results were compared with literature on the anatomy of humans, chimpanzees and baboons. In general, the enervation model of the four primates is identical, but in specific terms, the differences in enervations indicate evolution convergence closer to the branch of baboons in the evolutionary tree, and these data corroborate other comparative studies in relation to the same primates to vessels, muscles and nerves. In conclusion, the nerve organization in the thigh of C. libidinosus is identical to baboon, chimpanzee and homo, but more similar to baboon. The specific differences found indicate an ancient phylogenic origin to C. libidinosus and baboons (data corroborated by other studies).

scholarly journals Reexamination of Statistical Methods for Comparative Anatomy: Examples of Its Application and Comparisons with Other Parametric and Nonparametric Statistics

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Roqueline A. G. M. F. Aversi-Ferreira ◽  
Hisao Nishijo ◽  
Tales Alexandre Aversi-Ferreira
Keyword(s):  
Statistical Method ◽  
Statistical Methods ◽  
Comparative Anatomy ◽  
Nonparametric Statistics ◽  
Anatomical Structures ◽  
Parametric Test ◽  
Nonparametric Statistical Methods ◽  
Multiple Structures ◽  
Nonparametric Statistical ◽  
Parametric And Nonparametric Statistics

Various statistical methods have been published for comparative anatomy. However, few studies compared parametric and nonparametric statistical methods. Moreover, some previous studies using statistical method for comparative anatomy (SMCA) proposed the formula for comparison of groups of anatomical structures (multiple structures) among different species. The present paper described the usage of SMCA and compared the results by SMCA with those by parametric test (t-test) and nonparametric analyses (cladistics) of anatomical data. In conclusion, the SMCA can offer a more exact and precise way to compare single and multiple anatomical structures across different species, which requires analyses of nominal features in comparative anatomy.

Selection and Preparation of Specific Tissue Regions For Tem Using Large Epoxy-Embedded Blocks

1973 ◽  
Vol 31 ◽  
pp. 324-325 ◽  
Author(s):  
P. M. Lowrie ◽  
W. S. Tyler
Keyword(s):  
Electron Microscopy ◽  
Anatomical Structures ◽  
Ultrastructural Studies ◽  
Transmission Electron ◽  
Microscopic Evaluation ◽  
Embedded Blocks ◽  
Specific Tissue ◽  
Definition Of ◽  
Areas Of Interest ◽  
Selection Of

The importance of examining stained 1 to 2μ plastic sections by light microscopy has long been recognized, both for increased definition of many histologic features and for selection of specimen samples to be used in ultrastructural studies. Selection of specimens with specific orien ation relative to anatomical structures becomes of critical importance in ultrastructural investigations of organs such as the lung. The uantity of blocks necessary to locate special areas of interest by random sampling is large, however, and the method is lacking in precision. Several methods have been described for selection of specific areas for electron microscopy using light microscopic evaluation of paraffin, epoxy-infiltrated, or epoxy-embedded large blocks from which thick sections were cut. Selected areas from these thick sections were subsequently removed and re-embedded or attached to blank precasted blocks and resectioned for transmission electron microscopy (TEM).

ICERD in Malaysian online news reports: A cross-linguistic comparative corpus analysis

2019 ◽  
Vol 3 (4) ◽  
pp. 51
Author(s):  
Siti Aeisha Joharry ◽  
Nor Diyana Saupi
Keyword(s):  
Comparative Analysis ◽  
Public Discourse ◽  
Online News ◽  
Corpus Analysis ◽  
Search Term ◽  
International Convention ◽  
Online Newspapers ◽  
News Reports ◽  
The Media ◽  
Online Sources

The International Convention for the Elimination of Racial Discrimination (ICERD), which was not ratified in Malaysia, created a heated public discourse in the media. This cross-linguistic comparative study investigates the representation of ICERD in Malaysian news reports of two online sources in Malaysia – the widely read English portal: The Star Online, and its Malay equivalent: Berita Harian. A corpus-assisted discourse analysis was conducted to examine how news on ‘ICERD’ were reported in both English and Malay online newspapers. Initial comparative analysis of both newspapers revealed that the search term co-occurs statistically more frequently with the verb ‘ratify’ and its equivalent: ‘meratifikasi’. Patterns indicate that ‘ICERD’ was mostly referring to the act of sanctioning the agreement –particularly to ‘not ratify’ or ‘tidak akan meratifikasi’, which is concurrent with the timeframe of events. Interestingly, different patterns can be found in Berita Harian (e.g. the expression of ‘thanks’ or gratitude of not ratifying ICERD) that are not as revealing in The Star Online reports. Some inconsistencies were also reported between the two newspapers, e.g. referring to different ministers’ speech about the initial plan to ratify ICERD alongside five (The Star Online) or six (Berita Harian) other treaties in the following year.  

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