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10 results for “evolutionary knowledge”
Data from: Building on 150 years of knowledge: the freshwater isopod Asellus aquaticus as an integrative eco-evolutionary model system
<p><strong>Introduction</strong></p> <p>This is a literature database with reference information of all papers that use the freshwater isopod <em>Asellus aquaticus</em>; published between the years 1867 and 2020. This database is intended as a starting point for scientists interested in conducting research on and with this organism. The database is currently only available as a single CSV file; future versions may be made available through a more frequently updated SQL database. The database includes specific information about the subject area and content of each paper, as well as bibliographic information. This repository is associated with the paper "Building on 150 years of knowledge: the freshwater isopod<em> Asellus aquaticus</em> as an integrative eco-evolutionary model system", published in Frontiers in Ecology and Evolution.</p> <p><strong>Details on Methods from the electronic supplement:</strong></p> <p>We used the we online search tools of Web of Science (WOS; Clarivate analytics) by searching for the term "asellus aquaticus" in six relevant databases (BIOSIS, CABI, FSTA, Medline, WOS Core Collection and Zoological Records). The database was accessed with a University License (Lund University). We manually downloaded the results and combined them to a single CSV file in Excel (Microsoft). All further processing was done in the statistical programming language R, version 4.0.2 (R Core Team 2020).</p> <p>From the 1238 obtained records we discarded three papers that were published after the year 2020 to work with completed years only. We used the subject areas assigned by WOS to provide an overview of the fields of science in which A. aquaticus has been most studied. Each paper had between one and ten subject areas assigned by WOS (2845 assignments to 1235 papers, meaning 2.3 assignments per paper, on average). To represent these multiple assignments in relation to the actual number of papers per year, we calculated "fractional assignments" by adding up all assignments to a field per year, divided by the total number of assignments in that year, and then multiplied by the number of papers. For example, if there were 12 assignments to "toxicology" in 1993, and 133 assignments in 1993, but only 21 papers published, "toxicology" would get a score of 1.9 papers in 1993 (as calculated by = (12/133)*21). In Figure 1, we represent these "fractional assignments" in the top panel, and the total number of assignments in the lower panel.</p> <p><strong>Caption for figure (1) in publication:</strong></p> <p>FIGURE 1 | Over 150 years of research on and with Asellus aquaticus. The figure summarizes published scientific literature on A. aquaticus. We conducted a quantitative literature survey with the search tools of Web of Science (WOS; Clarivate analytics) by searching for the term "asellus aquaticus" in six databases (i.e., BIOSIS, CABI, FSTA, Medline, WOS Core Collection, and Zoological Records). We found 1235 records, published between 1867 and 2020. (A) The graph shows the number of publications per year within a given subject area, as designated by WOS. (B) The graph shows the total number of publications assigned to a specific subject area. The top 10 fields account for 72.58% of all publications, and are indicated by color coding in A and B (multiple assignments are possible, summing up to 2845 assignments). The inset in B shows a wordcloud with the 100 most used keywords from all A. aquaticus’ publications. Furthermore, we compiled all records with relevant information (e.g., title, keywords, research areas, and abstract) to a single file which is available online. More details can be found in the Supplementary Material.</p>
Figure 6 in State of knowledge of viviparity in Staphylinidae and the evolutionary significance of this phenomenon in Corotoca Schiødte, 1853
Figure 6. Scheme illustrating part of the life cycle of Corotoca sp. Left (A) shows hypothetical case of dispersion made by the adult, while the right (B) illustrates the hypothesis proposed in this work, of dispersion mainly by immature.
Figure 2 in State of knowledge of viviparity in Staphylinidae and the evolutionary significance of this phenomenon in Corotoca Schiødte, 1853
Figure 2. Estação Experimental São João do Cariri, located at São João do Cariri municipality, Paraiba State, northeastern of Brazil.
Figure 3 in State of knowledge of viviparity in Staphylinidae and the evolutionary significance of this phenomenon in Corotoca Schiødte, 1853
Figure 3. Corotoca phylo SchiØdte, 1853, female (= paratype of C. seeversi Fontes, 1977). (A) transversal cut of curvature of the abdomen, with two exposed eggs, each with an embryo in different stage of development in relation to another; (B) transversal cut od abdomen from segment IV, with exposed larva; (C) habitus lateral. Scales: 0.5 mm.
Supplement tables of Facilitating Antiviral Drug Discovery by Genetic and Evolutionary Knowledge
<p>Table S1: 36 human targets for approved antiviral drugs downloaded from Drugbank,</p> <p>Table S2: Supplementary information for Table 2,</p> <p>Table S3: Pockdrug druggability prediction results.</p>
Figure 1 in State of knowledge of viviparity in Staphylinidae and the evolutionary significance of this phenomenon in Corotoca Schiødte, 1853
Figure 1. Classification model for viviparous beetles.
Figure 5 in State of knowledge of viviparity in Staphylinidae and the evolutionary significance of this phenomenon in Corotoca Schiødte, 1853
Figure 5. Corotoca melantho SchiØdte, 1853, supposed second instar larva. Scale: 0.4 mm.
Data from: Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB; kb.phenoscape.org), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 639 variable characters scored for 1051 taxa, resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, that is, cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin-to-limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype-to-genome relationships.
Data from: Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies
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Figure 4 in State of knowledge of viviparity in Staphylinidae and the evolutionary significance of this phenomenon in Corotoca Schiødte, 1853
Figure 4. Corotoca melantho SchiØdte, 1853, female. (A) eggs from segment IV, each with an embryo in different stage of development in relation to another; (B) larva found in the apex of abdomen; (C) abdomen of female, lateral view. Scales: 0.5 mm.
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