It takes great effort to manually or semi-automatically convert free-text phenotype narratives (e.g., morphological descriptions in taxonomic works) to a computable format before they can be used in large-scale analyses. We argue that neither a manual curation approach nor an information extraction approach based on machine learning is a sustainable solution to produce computable phenotypic data that are FAIR (Findable, Accessible, Interoperable, Reusable) (Wilkinson et al. 2016). This is because these approaches do not scale to all biodiversity, and they do not stop the publication of free-text phenotypes that would need post-publication curation. In addition, both manual and machine learning approaches face great challenges: the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other) in manual curation, and keywords to ontology concept translation in automated information extraction, make it difficult for either approach to produce data that are truly FAIR. Our empirical studies show that inter-curator variation in translating phenotype characters to Entity-Quality statements (Mabee et al. 2007) is as high as 40% even within a single project. With this level of variation, curated data integrated from multiple curation projects may still not be FAIR. The key causes of this variation have been identified as semantic vagueness in original phenotype descriptions and difficulties in using standardized vocabularies (ontologies). We argue that the authors describing characters are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project's semantics and ontology. This will speed up ontology development and improve the semantic clarity of the descriptions from the moment of publication. In this presentation, we will introduce the Platform for Author-Driven Computable Data and Ontology Production for Taxonomists, which consists of three components: a web-based, ontology-aware software application called 'Character Recorder,' which features a spreadsheet as the data entry platform and provides authors with the flexibility of using their preferred terminology in recording characters for a set of specimens (this application also facilitates semantic clarity and consistency across species descriptions); a set of services that produce RDF graph data, collects terms added by authors, detects potential conflicts between terms, dispatches conflicts to the third component and updates the ontology with resolutions; and an Android mobile application, 'Conflict Resolver,' which displays ontological conflicts and accepts solutions proposed by multiple experts. a web-based, ontology-aware software application called 'Character Recorder,' which features a spreadsheet as the data entry platform and provides authors with the flexibility of using their preferred terminology in recording characters for a set of specimens (this application also facilitates semantic clarity and consistency across species descriptions); a set of services that produce RDF graph data, collects terms added by authors, detects potential conflicts between terms, dispatches conflicts to the third component and updates the ontology with resolutions; and an Android mobile application, 'Conflict Resolver,' which displays ontological conflicts and accepts solutions proposed by multiple experts. Fig. 1 shows the system diagram of the platform. The presentation will consist of: a report on the findings from a recent survey of 90+ participants on the need for a tool like Character Recorder; a methods section that describes how we provide semantics to an existing vocabulary of quantitative characters through a set of properties that explain where and how a measurement (e.g., length of perigynium beak) is taken. We also report on how a custom color palette of RGB values obtained from real specimens or high-quality specimen images, can be used to help authors choose standardized color descriptions for plant specimens; and a software demonstration, where we show how Character Recorder and Conflict Resolver can work together to construct both human-readable descriptions and RDF graphs using morphological data derived from species in the plant genus Carex (sedges). The key difference of this system from other ontology-aware systems is that authors can directly add needed terms to the ontology as they wish and can update their data according to ontology updates. a report on the findings from a recent survey of 90+ participants on the need for a tool like Character Recorder; a methods section that describes how we provide semantics to an existing vocabulary of quantitative characters through a set of properties that explain where and how a measurement (e.g., length of perigynium beak) is taken. We also report on how a custom color palette of RGB values obtained from real specimens or high-quality specimen images, can be used to help authors choose standardized color descriptions for plant specimens; and a software demonstration, where we show how Character Recorder and Conflict Resolver can work together to construct both human-readable descriptions and RDF graphs using morphological data derived from species in the plant genus Carex (sedges). The key difference of this system from other ontology-aware systems is that authors can directly add needed terms to the ontology as they wish and can update their data according to ontology updates. The software modules currently incorporated in Character Recorder and Conflict Resolver have undergone formal usability studies. We are actively recruiting Carex experts to participate in a 3-day usability study of the entire system of the Platform for Author-Driven Computable Data and Ontology Production for Taxonomists. Participants will use the platform to record 100 characters about one Carex species. In addition to usability data, we will collect the terms that participants submit to the underlying ontology and the data related to conflict resolution. Such data allow us to examine the types and the quantities of logical conflicts that may result from the terms added by the users and to use Discrete Event Simulation models to understand if and how term additions and conflict resolutions converge. We look forward to a discussion on how the tools (Character Recorder is online at http://shark.sbs.arizona.edu/chrecorder/public) described in our presentation can contribute to producing and publishing FAIR data in taxonomic studies.
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Key to the currently recognized species of Limnias Schrank, 1803 (Rotifera, Monogononta, Gnesiotrocha, Flosculariidae)
Although the most widely used key to the Rotifera subsumes six species of the sessile genus Limnias within two species groups (L. ceratophylli and L. melicerta), the original descriptions of these forms are sufficiently different to recognize them as distinct entities. We used these descriptions and all available literature on these species to develop dichotomous and formula keys to the six species based on easily recognizable morphological characters. As part of our review we added relevant ecological information from published sources, as well as our own data. We also discuss the need for additional observations of morphological, behavioral, life history, and genetic features to better understand the diversity of this widespread genus.
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- NSF-PAR ID:
- 10214778
- Date Published:
- Journal Name:
- Zootaxa
- Volume:
- 4442
- Issue:
- 2
- ISSN:
- 1175-5326
- Page Range / eLocation ID:
- 307; 318
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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The diatom genus
Entomoneis is known from the benthos and plankton of marine, brackish, and freshwaters.Entomoneis includes diatoms with a bilobate keel elevated above the valve surface, a sigmoid canal raphe, and numerous girdle bands. Owing mostly to the scarcity of molecular data for a diverse set of species, the phylogeny ofEntomoneis has not been investigated in depth. The few previous studies that includedEntomoneis were focused on broader questions and the available data were from a small number of either unidentifiedEntomoneis or well‐known species (e.g.,E. paludosa ). Since the first description of new species combining both molecular and morphological characters (E. tenera ), we have continued to cultivate and investigateEntomoneis in the plankton of the Adriatic Sea. Combined multigene phylogeny (SSU rDNA sequences,rbc L, andpsb C genes) and morphological observations (LM ,SEM andTEM ) revealed six newEntomoneis species supported by phylogenetic and morphological data:E. pusilla ,E. gracilis ,E. vilicicii ,E. infula ,E. adriatica, andE. umbratica . The most important morphological features for species delineation were cell shape, the degree and mode of torsion, valve apices, the appearance and structure of the transition between keel and valve body, the ultrastructure and the shape of the girdle bands, and the arrangement and density of perforations along the valve and valvocopulae. Our results highlight the underappreciated diversity ofEntomoneis and call for a more in‐depth morphological and molecular investigation of this genus especially in planktonic habitats. -
Supplementary descriptions are provided for six poorly known species of Caligus, based on a study of type and other material carried out by the late Roger F. Cressey but never published. As part of that study new illustrations were produced by Hillary Boyle Cressey who has kindly made these previously unpublished drawings available to this paper. The present account also contains critical re-assessments of the validity of several other species of Caligus Müller, 1785. It is proposed to recognise that: C. glacialis Gadd, 1910 and C. raniceps Heegaard, 1943 are junior subjective synonyms of the type species C. curtus Müller, 1785 and we consider the published geographical locality given for C. raniceps by Heegaard (1943) to be erroneous; C. guerini Guiart, 1913 is a junior subjective synonym of C. elongatus von Nordmann, 1832; C. mordax Leigh-Sharpe, 1934 is a junior subjective synonym of C. coryphaenae Steenstrup & Lütken, 1861; C. lessonius Risso, 1826 is not a caligid and is probably a junior synonym of the pandarid Demoleus heptapus (Otto, 1821); C. clavatus Kirtisinghe, 1964 is a junior subjective synonym of C. sphyraeni Pillai, 1963; C. rotundigenitalis Yü, 1933 is a junior subjective synonym of C. torpedinis Heller, 1865; C. hyalinae Heegaard, 1966 is a junior subjective synonym of C. chelifer Wilson, 1905; C. biseriodentatus, Shen, 1957 is a junior subjective synonym of C. pauliani Nuñes-Ruivo & Fourmanoir, 1956; and C. cornutus Heegaard, 1962 can be formally treated as a junior subjective synonym of C. lobodes (Wilson, 1911) because the name C. cornutus belongs with the male holotype; the female allotype collected by Heegaard (1962) remains unidentified. We also conclude that C. mebachii Marukawa, 1927 was based on a young male of Euryphorus brachypterus (Gerstaecker, 1853) and a male of Caligus coryphaenae Steenstrup & Lütken, 1861 which was mistakenly identified as the female. A lectotype is designated for C. mebachii and this species is treated as a synonym of Euryphorus brachypterus. It is noted that C. hamatus Heegaard, 1955 is conspecific with, and has priority over, C. undulatus Shen & Li, 1959. However, given that C. undulatus is a high profile and well known species, frequently recorded from across the Pacific, Indian and Atlantic oceans, a case has been submitted to the ICZN to grant precedence of C. undulatus over C. hamatus. We reject the transfer of Chalimus tenuis Leidy, 1889 to Caligus by Fowler (1912) on the basis of lack of evidence supporting the transfer, and return it to Chalimus, where it can be treated as a species inquirendum within a genus that is no longer considered as valid. We consider that C. alalongae Krøyer, 1863 and C. gracilis Dana, 1852 are species inquirenda. Caligus truttae is a nomen nudum because Giard (1890) provided no morphological information or illustration associated with the new name.more » « less
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The Peruvian genera of Edrotini (Pimeliinae) are revised. A new genus Pachacamacius Flores & Giraldo gen. nov. with two new species, Pachacamacius aguilari Giraldo & Flores sp. nov. (type species) and Pachacamacius koepckeae Flores & Giraldo sp. nov., is described. Two species originally described in the genus ProhylithusKaszab, 1964 are reassigned to two new monotypic genera: Sechuranus Flores and Giraldo gen. nov. (type species Prohylithus barbatusKaszab, 1964) and Koneus Giraldo and Flores, gen. nov. (type species Prohylithus peruanusKaszab, 1981). This article includes diagnoses for five genera and redescriptions or descriptions, distributional data, habitat records and habitus photographs for six species. A dichotomous key for all 11 Peruvian species of Edrotini, drawings of new species' male genitalic features, and distribution maps are also provided. A discussion of the external morphological characters and male genitalia of the new taxa compared to the genera and species previously described and on endemicity and zoogeography of Peruvian Edrotini is presented.more » « less
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Abstract Three new cestode species are described from the crocodile shark ( Pseudocarcharias kamoharai ) in Ecuador. All three were examined with light and scanning electron microscopy. The unique combination of morphological features in one of the new species prompted formal investigation of the non-monophyly of Paraorygmatobothrium relative to the morphologically similar genera Doliobothrium , Guidus , Marsupiobothrium , Nandocestus , Orectolobicestus , Ruhnkecestus and Scyphophyllidium . Sequence data generated for part of the 28S rDNA gene were subjected to maximum likelihood (ML) analysis. The resulting tree led to the synonymization of six of these seven genera with Scyphophyllidium , and transfer of their species to the latter genus. With the new species, the number of described members of Scyphophyllidium is now 45. The diagnosis of Scyphophyllidium is revised to accommodate these species. In addition, to expedite future descriptions, eight categories of Scyphophyllidium species are circumscribed, based largely on bothridial features. Scyphophyllidium timvickiorum n. sp. is a category 1 species. Beyond being the smallest category 1 species, it bears, rather than lacks, apical suckers and lacks, rather than bears, strobilar scutes. The two other new species are members of Clistobothrium . Clistobothrium amyae n. sp. differs from its congeners in bothridial shape, elongate cephalic peduncle and tiny size. Clistobothrium gabywalterorum n. sp. differs from the two of its congeners that also possess foliose bothridia in overall size and testis number. Despite their substantial morphological differences, the ML tree indicates they are sister taxa. Both are unique among their congeners in possessing cephalic peduncle spinitriches. The diagnosis of Clistobothrium is revised accordingly.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.11646/zootaxa.4442.2.7
