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949 results for “species names”
Linked collectors and determiners for: Scrophularia longiflora Benth. and S. nana Stiefelh. (Scrophulariaceae), two distinct species from Iran, confused under the name S. farinosa Boiss..
Natural history specimen data linked to collectors and determiners held within, "Scrophularia longiflora Benth. and S. nana Stiefelh. (Scrophulariaceae), two distinct species from Iran, confused under the name S. farinosa Boiss.". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/d37b25f7-6746-4dee-9a0c-dc690e951707">https://bionomia.net/dataset/d37b25f7-6746-4dee-9a0c-dc690e951707</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/d37b25f7-6746-4dee-9a0c-dc690e951707">https://gbif.org/dataset/d37b25f7-6746-4dee-9a0c-dc690e951707</a>. Formatted as a Frictionless Data package.
FIG. 3 in On the distinction of Atractocarpus heterophyllus (Montrouz.) Guillaumin & Beauvis. and A. bracteatus Schltr. & K.Krause (Rubiaceae): in search of the correct name for the type species of Atractocarpus Schltr. & K.Krause
FIG. 3. — Atractocarpus heterophyllus (Montrouz.) Guillaumin & Beauvis.: A, view of the apex of a female individual in fruit; B, detail of stipules at branch apex; C, transversal section of a fruit; D, longitudinal section of a fruit; E, developed placenta at fruit stage, in dorsal and ventral views; F, longitudinal section of a seed; G, embryo. Scale bars: A-E, 3 cm; F, G, 2 mm. Based on MacKee 26464 (P) and unpublished N. Hallé's drawings of New Caledonian Rubiaceae in sched (P).
FIG. 2 in On the distinction of Atractocarpus heterophyllus (Montrouz.) Guillaumin & Beauvis. and A. bracteatus Schltr. & K.Krause (Rubiaceae): in search of the correct name for the type species of Atractocarpus Schltr. & K.Krause
FIG. 2. — Atractocarpus bracteatus Schltr. & K.Krause: A, female flower; B, longitudinal section of a female flower (corolla and stamens detached from hypanthium); C, detail of stipules at branch apex; D, entire fruit and longitudinal section of a fruit; E, transversal section of a fruit; F, entire seed and its longitudinal section; G, embryo. Scale bars: A-C, 1.5 cm; D, 6 cm; E, 1.5 cm; F, 5 mm; G, 2 mm. Based on Mouly 149 (P).
FIG. 1 in On the distinction of Atractocarpus heterophyllus (Montrouz.) Guillaumin & Beauvis. and A. bracteatus Schltr. & K.Krause (Rubiaceae): in search of the correct name for the type species of Atractocarpus Schltr. & K.Krause
FIG. 1. — Atractocarpus bracteatus Schltr. & K.Krause: A, view of a female individual in fruit; B, male inflorescence, and detail of a flower with ant; C, mature fruit. Scale bars: A, 10 cm; B, C, 1 cm. Based on pictures by Daniel & Irène Létocart (www.endemia.nc).
FIG, 1. John William Daly (1933–2008) on the upper Río San Juan. This paper is dedicated to John Daly, our late friend and colleague, who helped collect three of the new species here described. In addition to his globally acclaimed discoveries in chemistry and pharmacology, John was an accomplished field herpetologist who contributed importantly to the systematics and natural history of dendrobatoid frogs (see Grant et al., 2006; Myers, 2009). This photograph shows John at age 37, with the upper Río San Juan behind him and branches overhead of a madroño tree (probably Garcinia magnifolia, syn. Rheedia chocoensis, Clusiaceae). When in South America, John was never far from a dendrobatid frog—this time, in the tree above his head, a tiny, undescribed semiarboreal species (also collected and later named "Dendrobates fuguritus" by our colleague Philip Silverstone). Other dendrobatids found nearby included Phyllobates aurotaenia (Boulenger, 1913), which was then being used for poisoning blowgun darts, and also the nontoxic species that we name Silverstoneia dalyi herein. (Photograph by C. W. Myers, 2 km above Playa de Oro, Chocó, February 16, 1971.) in Review of the Frog Genus Silverstoneia, with Descriptions of Five New Species from the Colombian Chocó (Dendrobatidae: Colostethinae)
FIG, 1. John William Daly (1933–2008) on the upper Río San Juan. This paper is dedicated to John Daly, our late friend and colleague, who helped collect three of the new species here described. In addition to his globally acclaimed discoveries in chemistry and pharmacology, John was an accomplished field herpetologist who contributed importantly to the systematics and natural history of dendrobatoid frogs (see Grant et al., 2006; Myers, 2009). This photograph shows John at age 37, with the upper Río San Juan behind him and branches overhead of a madroño tree (probably Garcinia magnifolia, syn. Rheedia chocoensis, Clusiaceae). When in South America, John was never far from a dendrobatid frog—this time, in the tree above his head, a tiny, undescribed semiarboreal species (also collected and later named "Dendrobates fuguritus" by our colleague Philip Silverstone). Other dendrobatids found nearby included Phyllobates aurotaenia (Boulenger, 1913), which was then being used for poisoning blowgun darts, and also the nontoxic species that we name Silverstoneia dalyi herein. (Photograph by C. W. Myers, 2 km above Playa de Oro, Chocó, February 16, 1971.)
TYPES: Male holotype from Panama: Panama: Parque Nacional Altos de Campana, 1 hectare PANCODING Inventory, 895 m, 8.68333°, -79.92972°, June 14–19, 2007, M. Arnedo, D. Dimitrov, G. Hormiga, F. Labarque, M. Ramírez, deposited in MIUP, PBI_OON 42313; same data, 1 male paratype deposited in MACN-Ar 29895, PBI_OON 42312. ETYMOLOGY: A noun in apposition; in Greek religion and mythology, Pan is the god of the wild natural world, of shepherds, flocks, and mountains, and of hunting and rustic music. He has hindquarters, legs, and horns of a goat, and the name is here employed to note the large mac- rosetae at the eye region of males that resemble the horns in some illustrations of this god. DIAGNOSIS: This is one of the most autapomor- phic species from the Americas; males have the labium fused with the sternum (fig. 34B), small chelicerae, shorter than the endite length, with anterior blunt projections, and directed backward in lateral view (fig. 34D, E); clypeus directed back- ward (fig. 34D); two light areas on the sternum just below the endites (fig. 34B), carapace almost flat in lateral view and two strong macrosetae at the eye region, pointing forward (fig. 34C–E). Other characters of the male palp, such as the presence of two apophyses, also distinguish this species from others (fig. 38D–F). MALE (PBI_OON 42312): Total length 1.00. Habitus as in figure 34A–C. CEPHALOTHO- RAX: Carapace orange, with brown stripe along in Taxonomic Revision Of The Jumping Goblin Spiders Of The Genus Orchestina Simon, 1882, In The Americas (Araneae: Oonopidae)
TYPES: Male holotype from Panama: Panama: Parque Nacional Altos de Campana, 1 hectare PANCODING Inventory, 895 m, 8.68333°, -79.92972°, June 14–19, 2007, M. Arnedo, D. Dimitrov, G. Hormiga, F. Labarque, M. Ramírez, deposited in MIUP, PBI_OON 42313; same data, 1 male paratype deposited in MACN-Ar 29895, PBI_OON 42312. ETYMOLOGY: A noun in apposition; in Greek religion and mythology, Pan is the god of the wild natural world, of shepherds, flocks, and mountains, and of hunting and rustic music. He has hindquarters, legs, and horns of a goat, and the name is here employed to note the large mac- rosetae at the eye region of males that resemble the horns in some illustrations of this god. DIAGNOSIS: This is one of the most autapomor- phic species from the Americas; males have the labium fused with the sternum (fig. 34B), small chelicerae, shorter than the endite length, with anterior blunt projections, and directed backward in lateral view (fig. 34D, E); clypeus directed back- ward (fig. 34D); two light areas on the sternum just below the endites (fig. 34B), carapace almost flat in lateral view and two strong macrosetae at the eye region, pointing forward (fig. 34C–E). Other characters of the male palp, such as the presence of two apophyses, also distinguish this species from others (fig. 38D–F). MALE (PBI_OON 42312): Total length 1.00. Habitus as in figure 34A–C. CEPHALOTHO- RAX: Carapace orange, with brown stripe along
Figs 15-22 in Six new species, a new name, and additional records of Lathrobium from the Palaearctic region (Coleoptera: Staphylinidae: Paederinae)
Figs 15-22: Lathrobium unguiferum nov.sp.: (15) forebody; (16) head in lateral view; (17) male sternite VII; (18) male sternite VIII; (19-20) aedeagus in lateral and in ventral view; (21) female sternite VIII; (22) female abdominal segments IX-X. Scale bars: 15: 1.0 mm; 16-22: 0.5 mm.
Figs 39-45 in Six new species, a new name, and additional records of Lathrobium from the Palaearctic region (Coleoptera: Staphylinidae: Paederinae)
Figs 39-45: Lathrobium wolongicum nov.sp.: (39) male forebody; (40) male sternite VII; (41) male sternite VIII; (42-45) aedeagus in lateral and in ventral view in transparent light (42-43) and in dry preparation (44-45). Scale bars: 39: 1.0 mm; 40-45: 0.5 mm.
Figs 30-38 in Six new species, a new name, and additional records of Lathrobium from the Palaearctic region (Coleoptera: Staphylinidae: Paederinae)
Figs 30-38: Lathrobium jiajinum nov.sp.: (30) male forebody; (31) male sternite VII; (32) male sternite VIII; (33-36) aedeagus in lateral and in ventral view in transparent light (33-34) and in dry preparation (35-36); (37) female sternite VIII; (38) female abdominal segments IX-X. Scale bars: 30: 1.0 mm; 31-38: 0.5 mm.
Figs 23-29 in Six new species, a new name, and additional records of Lathrobium from the Palaearctic region (Coleoptera: Staphylinidae: Paederinae)
Figs 23-29: Lathrobium spinans nov.sp.: (23) forebody; (24) male sternite VII; (25) male sternite VIII; (26-27) aedeagus in lateral and in ventral view; (28) female sternite VIII; (29) female abdominal segments IX-X. Scale bars: 23: 1.0 mm; 24-25, 28-29: 0.5 mm; 26-27: 0.2 mm.
Figs 1-7 in Six new species, a new name, and additional records of Lathrobium from the Palaearctic region (Coleoptera: Staphylinidae: Paederinae)
Figs 1-7: Lathrobium kociani nov.sp.: (1) forebody; (2) head in dorsal view; (3) head in lateral view; (4) male sternite VII; (5) male sternite VIII; (6-7) aedeagus in lateral and in ventral view. Scale bars: 1: 1.0 mm; 2-5: 0.5 mm; 6-7: 0.2 mm.
Figs 8-14 in Six new species, a new name, and additional records of Lathrobium from the Palaearctic region (Coleoptera: Staphylinidae: Paederinae)
Figs 8-14: Lathrobium makaluicum ASSING (8-9) and L. retunsum nov.sp. (10-14): (8) female sternite VIII; (9) female abdominal segments IX-X; (10) forebody; (11) male sternite VII; (12) male sternite VIII; (13-14) aedeagus in lateral and in ventral view. Scale bars: 10: 1.0 mm; 8-9, 11- 14: 0.5 mm.
Fig. 1 in Octopus sinensis d'Orbigny, 1841 (Cephalopoda: Octopodidae): Valid Species Name for the Commercially Valuable East Asian Common Octopus
Fig. 1. Ventral view of a mature male specimen of Octopus sinensis (NSMT Mo 85658), illustrating the paler ventral surface (cf. dorsal surface of the same specimen visible in Figs 2 and 3) and the size and shape of the funnel (F, held in place with a piece of white cord). A sample (S) of muscle tissue was removed prior to fixation, leaving a circular wound just anterior to the funnel. Fig. 2. Dorsal view of the specimen in Fig. 1, showing the difference in lengths of arms 2 and 3 (longer, ending within the region labelled 'Arms 2 and 3' bracketed to the leπ) versus 1 and 4 (clearly shorter, ending within the adjacent bracketed region labelled 'Arms 1 and 4'). The longer arms include arm R3 (the hectocotylus, H), which (typically much shorter than its counterpart, L3) is only just a little longer than arm pairs 1 and 4 (cf. Table 1, and OAI in Table 2). Note also the relative size and shape of the head, body and arms, and the rugose texture caused by the fixed appearance of the patch-and-groove topology of the skin. Fig. 3. View from the right side (body to leπ; arms to right) of the specimen in Figs 1 and 2. The funnel (F) was fixed in an unusual position (here seen pointing ventrally, perpendicular to the main body axis) as a result of damage following removal (before fixation) of a tissue sample (S) for molecular analysis (cf. Fig. 1). The broad extent of the mantle opening can be seen ventrally. Dorsally there is a large, contracted posterodorsal papilla (Ppd) above the right eye, with a smaller one anterodorsally (Pad). The anterodorsal papilla typically is not obvious except in well-fixed specimens. Fig. 4. An example of the appearance of the oral surface of a male Octopus sinensis to show the position of specially enlarged suckers on arms 2 and 3 of each side (most obvious on arms 2, as indicated: suckers #12 and 13 on the leπ, and #13 and 14 on the right). Anterior of animal (Ant.) is to the leπ, so the leπ arms are in the upper half of the figure and the right arms in the lower half. (Neotype specimen NSMT Mo 85659). Fig. 5. End of arm R3 of the specimen in Figs 1–3, showing the robust spermatophore groove (SGr; cf. Fig. 2, H) and small ligula (L). Fig. 6. Diagram of the tip of arm R3 of Octopus sinensis (lot NSMT Mo 85660 specimen IGG 318, ML 168 mm), illustrating the form of the ligula in more detail. Note modest calamus (Cal.) nestled in the hilum at the base of the ligula, and protuberance (Pr.) on the anterior side closely apposed to the region at the end of the spermatophore groove (SGr), covering the base of both ligula and calamus. (Line drawing by Aki Hamamoto). Fig. 7. Diagram of the tip of arm R3 of Octopus vulgaris specimen BMNH 98.5.21.346 (ML 96 mm), showing that the form and size of the ligula are similar to those of the ligula of O. sinensis (as shown in Figs 5 and 6). (Line drawing by Aki Hamamoto)
Fig. 1 in Two New Species of Lecithotrophic Nauplius y with Remarkable Labra from Okinawa, Japan, and a Family-Group Name for y-Larvae (Crustacea: Thecostraca: Facetotecta: Hansenocarididae fam. nov.)
Fig. 1. Hansenocaris cristalabri sp. nov., holotype (NHMD-1174614), microphotographs of living nauplius at two different stages of development. A, B, nauplius in dorsal and lateral view, respectively; C, D, last-stage nauplius in ventral and lateral view, respectively. Live video of H. cristalabri sp. nov. can be seen here: https://youtu.be/SCskuhPTCXo and is also deposited at Figshare.com: https://doi.org/10.6084/ m9.figshare.20430807.
Fig. 3 in Two New Species of Lecithotrophic Nauplius y with Remarkable Labra from Okinawa, Japan, and a Family-Group Name for y-Larvae (Crustacea: Thecostraca: Facetotecta: Hansenocarididae fam. nov.)
Fig. 3. Hansenocaris cristalabri sp. nov., holotype (NHMD-1174614), scanning electron micrographs of last-stage nauplius. A, B, habitus, dorsal and posteriodorsal view respectively; C, cephalic shield, slightly oblique frontal view, with 'primordial plates' differentiated by colors and abbreviations following Itô's (1987b, 1990) system (see Fig. 4); D–M, details of pores and setae of cephalic shield in A and C, indicated by dotted arrows; N, detail of spine-flanked notch in posterolateral margin of cephalic shield, indicated by dotted arrow (cf. Fig. 2E); O, two orderly spine-rows defining dorsal "keel" of trunk and contrasting with otherwise irregularly arranged spinules of transverse ridges. Abbreviations: C, crescentic plate; F-1–F-4, derivatives of primordial frontal plates 1–4; I-1, intercalary plate 1; O-1, occipital plate 1; P-1, derivatives of primordial polygonal plate 1; W, window; pores and setae numbered as described in text and Table 1.
Fig. 2 in Two New Species of Lecithotrophic Nauplius y with Remarkable Labra from Okinawa, Japan, and a Family-Group Name for y-Larvae (Crustacea: Thecostraca: Facetotecta: Hansenocarididae fam. nov.)
Fig. 2. Hansenocaris cristalabri sp. nov., holotype (NHMD-1174614), scanning electron micrographs of last-stage nauplius. A, B, habitus, ventral and lateral views, respectively; C, D, cockscomb-like labral process, left (enlarged from B) and right-posterior views, respectively; E, detail of spine-flanked notch in posteriolateral margin of cephalic shield, indicated by dotted arrow (cf. Fig. 3N); F, G, successively enlarged details of pore in A on posterior face of labral base, indicated by dotted arrows; H, detail of pore in A indicated by dotted arrow; I–M, details of pores in B indicated by dotted arrows; N, same as E; O, detail of dorsocaudal spine in B, left lateral view; P, detail of region of furcal spines, slightly oblique ventral view. Abbreviations: invag, cuticular invagination; pores and setae numbered as described in text and Table 1.
Fig. 5 in Two New Species of Lecithotrophic Nauplius y with Remarkable Labra from Okinawa, Japan, and a Family-Group Name for y-Larvae (Crustacea: Thecostraca: Facetotecta: Hansenocarididae fam. nov.)
Fig. 5. Hansenocaris cristalabri sp. nov., holotype (NHMD-1174614), scanning electron micrographs of last-stage nauplius. A, naupliar appendages (first antennae, second antennae, and mandibles) and labrum with cockscomb-like process, ventral view; B, same, anterior view; C, left first antennae, outer side; D, right second antenna, inner side; E, F, left mandible, viewed from two different angles. Abbreviations: ba, basis; co, coxa; en, endopod; ex, exopod; invag, cuticular invagination. Arabic numerals 1–6, exopodal segments 1–6, numbered from proximal to distal.
Fig. 4 in Two New Species of Lecithotrophic Nauplius y with Remarkable Labra from Okinawa, Japan, and a Family-Group Name for y-Larvae (Crustacea: Thecostraca: Facetotecta: Hansenocarididae fam. nov.)
Fig. 4. Comparison of cephalic shield plates of Hansenocaris furcifera Itô, 1989 and Hansenocaris cristalabri sp. nov., holotype (NHMD- 1174614). A–E, cephalic shields of last five naupliar instars [N1–N5 respectively according to Itô (1990)] of H. furcifera with color-zone indications (key at lower right) showing successive stages of subdivision of shield plates (facets) starting with 'primordial' plates in N1 (after Itô 1987a, 1990: figs 5E–F, 7, 8E, 10B; used with permission of the editor, Publications of the Seto Marine Biological Laboratory); F, last-stage nauplius of Hansenocaris cristalabri sp. nov. with presumed plate homologies to H. furcifera indicated by color-coding and alpha-numeric labels. Putatively homologous regions in C, E, and F marked by linked dotted ellipses.
LivingNER corpus: Named entity recognition, normalization & classification of species, pathogens and food
<p><strong>LivingNER Gold Standard corpus (includes training, validation, test and background sets + MULTILINGUAL RESOURCES</strong>)</p><p> </p><p><strong>Please cite if you use this dataset:</strong></p><p>A. Miranda-Escalada, E. Farré-Maduell, S. Lima-López, D. Estrada, L. Gascó, M. Krallinger, Mention detection, normalization & classification of species, pathogens, humans and food in clinical documents: Overview of LivingNER shared task and resources, <i>Procesamiento del Lenguaje Natural</i> (2022)</p><p>@article{amiranda2022nlp, title={Mention detection, normalization \& classification of species, pathogens, humans and food in clinical documents: Overview of LivingNER shared task and resources}, author={Miranda-Escalada, Antonio and Farr{\'e}-Maduell, Eul{`a}lia and Lima-L{\'o}pez, Salvador and Estrada, Darryl and Gasc{\'o}, Luis and Krallinger, Martin}, journal = {Procesamiento del Lenguaje Natural}, year={2022} }</p><p> </p><p><i><strong>1. Introduction</strong></i></p><p>The LivingNER Gold Standard corpus is a collection of<strong> 2000 clinical case reports</strong> covering a <strong>broad range of medical specialities</strong>, i.e. infectious diseases (including Covid-19 cases), cardiology, neurology, oncology, dentistry, pediatrics, endocrinology, primary care, allergology, radiology, psychiatry, ophthalmology, urology, internal medicine, emergency and intensive care medicine, tropical medicine, and dermatology <strong>annotated with species</strong> [SPECIES] (including <strong>living organisms</strong> and <strong>microorganisms</strong>) and <strong>infectious diseases</strong> [ENFERMEDAD] mentions. Species mentions include many <strong>pathogens</strong> and infectious agents, but also <strong>food</strong>, allergens, <strong>pets</strong> or other species, taxonomic groups and organisms of clinical relevance. </p><p>The LivingNER corpus has also annotations of mentions of <strong>humans</strong> (tag HUMAN), including the patients itself, <strong>family members</strong>, healhcare professionals or other persons mentioned in the case reports. Thus it can be useful to extract family history information of patients or information about the social and healthcare personal environment and interactions.</p><p>All mentions have been exhaustively manually mapped by experts to their corresponding <a href="https://www.ncbi.nlm.nih.gov/taxonomy"><strong>NCBI Taxonomy</strong></a> identifiers. </p><p>It was used for the <a href="https://temu.bsc.es/livingner/">LivingNER</a> Shared Task on pathogens and living beings detection and normalization in Spanish medical documents, which was celebrated as part of IberLEF 2022.</p><p> </p><p><i><strong>2. Training, validation, test and background sets</strong></i></p><p>The training set is composed of 1000 clinical case reports. The validation set includes 500 clinical case reports with the same characteristics and the test set includes 485. The background set is a collection of around 13k unannotated case reports that were originally added to prevent manual annotations in the test set during the competition and to create a Silver Standard.</p><p><i><strong>2.1 Annotations format</strong></i></p><p>Annotations and text files are distributed separately. The texts are in plain text (.txt in UTF-8) format, while the annotations are are distributed in a tab-separated file (.tsv) file with one row per annotation:</p><p>- For <strong>subtask 1 (LivingNER-Species NER track)</strong>, the .tsv file has the following columns:</p><ul><li>filename: document name</li><li>mark: identifier mention mark</li><li>label: mention type (SPECIES or HUMAN)</li><li>off0: starting position of the mention in the document</li><li>off1: ending position of the mention in the document</li><li>span: textual span</li></ul><p> - For <strong>subtask 2 (LivingNER-Species Norm track)</strong>, the .tsv file has the same columns as the previous one, plus:</p><ul><li>isH: whether the span is narrower than the NCBITax assigned code</li><li>isN: whether the mention corresponds to a nosocomial infection</li><li>iscomplex: whether the span has assigned a combination of NCBITax codes</li><li>NCBITax: mention code in the NCBI Taxonomy</li></ul><p>- For <strong>subtask 3 (LivingNER-Clinical IMPACT track)</strong>, the .tsv file has the following columns:</p><ul><li>filename</li><li>isPet (Yes/No)</li><li>PetIDs (NCBITaxonomy codes of pet & farm animals present in document)</li><li>isAnimalInjury (Yes/No)</li><li>AnimalInjuryIDs (NCBITaxonomy codes of animals causing injuries present in document)</li><li>IsFood (Yes/No)</li><li>FoodIDs (NCBITaxonomy codes of food mentions present in document)</li><li>isNosocomial (Yes/No)</li><li>NosocomialIDs (NCBITaxonomy codes of nosocomial species mentions present in document)</li></ul><p><i><strong>2.2 Important notes about subtask 3 (LivingNER-Clinical IMPACT track):</strong></i></p><ul><li><strong>Less clinical case reports</strong>. Subtask 3 (LivingNER-Clinical IMPACT track) contains half of the clinical case reports (500 in the training partition, 250 in the validation partition). The list of valid clinical case reports for task 3 is included in the data (train_files_task3.txt and validation_files_task3.txt)</li><li><strong>Enriched dataset.</strong> The GS format is the one described above (a TSV with one line per clinical case report). However, we believe participants may find useful and <strong>enriched dataset. </strong>Then, we provide an additional dataset, with the mentions of the NER track classified in the 4 Clinical impact categories (food, pet&farm animals, animals causing injuries and nosocomial). It is a TSV file with one row per annotation, and with the following columns: filename, mark, label, off0, off1, span, isPet, isAnimalInjury, isFood, isNosocomial, isH, iscomplex, code</li></ul><p> </p><p><i><strong>3. Multilingual resources</strong></i></p><p>We have generated the annotated training and validation sets in <strong>7 languages</strong>:</p><ul><li><i><strong>English</strong></i></li><li><i><strong>Portuguese</strong></i></li><li><i><strong>Catalan</strong></i></li><li><i><strong>Galician</strong></i></li><li><i><strong>Italian</strong></i></li><li><i><strong>French</strong></i></li><li><i><strong>Romanian</strong></i></li></ul><p> </p><p>The process was:</p><ol><li>The text files were translated with a neural machine translation system.</li><li>The annotations were translated with the same neural machine translation system.</li><li>The translated annotations were transferred to the translated text files using an annotation transfer technology.</li></ol><p>The text files are stored in the multilingual_resources/<strong>training-text-files</strong> and multilingual_resources/<strong>validation-text-files </strong>subfolders.</p><p>The annotated TSV files are stored in the multilingual_resources/<strong>annotation_transfer </strong>subfolder.</p><p>For the sake of comparison, we incorporate as well the annotations that resulted from the <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-85">LINNAEUS tool</a> in the multilingual_resources/<strong>linneaus</strong> subfolder.</p><p>If you want to visualize the multilingual resources, check out this Brat server: <a href="https://temu.bsc.es/mLivingNER/#/translations/">https://temu.bsc.es/mLivingNER/#/translations/</a></p><p>For instance, you can see the parallel annotations in <a href="https://temu.bsc.es/mLivingNER/diff.xhtml#/translations/en/annotation_transfer/train/casos_clinicos_cardiologia34?diff=/translations/fr/annotation_transfer/train/">English vs in French</a>, or <a href="https://temu.bsc.es/mLivingNER/diff.xhtml#/translations/cat/annotation_transfer/train/casos_clinicos_cardiologia35?diff=/gold-standard/train/">in Spanish (the gold standard) vs in Catalan.</a></p><p> </p><p><strong>Resources</strong></p><ul><li><a href="https://temu.bsc.es/livingner/"><strong>Task Web</strong></a></li><li><strong>Citation: </strong>A. Miranda-Escalada, E. Farré-Maduell, S. Lima-López, D. Estrada, L. Gascó, M. Krallinger, Mention detection, normalization & classification of species, pathogens, humans and food in clinical documents: Overview of LivingNER shared task and resources, <i>Procesamiento del Lenguaje Natural</i> (2022)</li><li><a href="https://doi.org/10.5281/zenodo.6385162"><strong>Annotation guidelines</strong></a></li><li><a href="https://github.com/tonifuc3m/livingner-evaluation-library"><strong>Evaluation library</strong></a></li><li><a href="https://doi.org/10.5281/zenodo.6390506">LivingNER terminology</a></li><li><a href="http://journal.sepln.org/sepln/ojs/ojs/index.php/pln/article/view/6444"><strong>Overview paper</strong></a></li><li><a href="https://ceur-ws.org/Vol-3202/"><strong>Proceedings participant papers</strong></a></li><li><a href="https://www.youtube.com/watch?v=8VcZw8ywyJY&list=PL5uSCzf1azhA_gMLC3DBZe6NvmMJiggTg"><strong>Youtube videos</strong></a></li><li><a href="https://www.slideshare.net/MartinKrallinger/mention-detection-normalization-classification-of-species-pathogens-humans-and-food-in-clinical-documents-overview-of-the-livingner-shared-task-and-resources-talk-at-iberlef-sepln-2022"><strong>LivingNER overview talk sides at IberLEF/SEPLN</strong></a></li></ul><p> </p><p><strong>License</strong></p><p>This work is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p><p><strong>Contact</strong></p><p>If you have any questions or suggestions, please contact us at:</p><p><br>- Martin Krallinger (<krallinger [dot] martin [at] gmail [dot] com>)</p><p><strong>Additional resources and corpora</strong></p><p>If you are interested in SympTEMIST, you might want to check out these corpora and resources:</p><ul><li><a href="https://zenodo.org/records/7614764">DisTEMIST</a> (Corpus of disease mentions and normalization to SNOMED CT, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/8413866">SympTEMIST</a> (Corpus of symptoms, sign and findings mentions and normalization to SNOMED CT, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/8224056">MedProcNER </a>(Corpus of clinical procedure mentions and normalization to SNOMED CT, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/4270158">PharmaCoNER</a> (Corpus of medications, drugs, chemical substances, genes, proteins and vaccine mentions and normalization, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/7116201">MEDDOPROF</a> (Corpus of mentions of professions, occupations and working status and normalization, different document collection)</li><li><a href="https://zenodo.org/records/8403498">MEDDOPLACE</a> (Corpus of mentions of place-related entity mentions, including departments, nationalities or patient movements etc.. and normalization, different document collection)</li><li><a href="https://zenodo.org/records/4279323">MEDDOCAN</a> (Corpus of mentions of Personal Health Identifiers (PHI), differentdocument collection)</li><li><a href="https://zenodo.org/records/3978041">CANTEMIST</a> (Corpus of cancer tumor morphology mentions and normalization, different document collection)</li><li><a href="https://zenodo.org/records/3837305">CodiESp</a> (Corpus of clinical case reportes with assigned clinical codes from ICD10, Spanish version, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/2560344">SPACCC-POS</a> (Corpus of clinical case reports in Spanish annotated with POS-tags, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/2560338">SPACCC-TOKEN</a> (Corpus of clinical case reports in Spanish annotated with token-tags (word mention boundaries), different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/2560338">SPACCC-SPLIT</a> (Corpus of clinical case reports in Spanish annotated with sentence boundary-tags, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/5602914">MESINESP-2</a> (Corpus of manually indexed records with DeCS /MeSH terms comprising scientific literature abstracts, different document collection, some overlapping documents)</li></ul>
Figure 6. Pseudophycis bachus. A, B, NMNZ P.054828 in A review of the Australasian genus Pseudophycis (Gadiformes: Moridae), redescribing its four species and resurrecting the name Physiculus palmatus Klunzinger, 1872, for the Australian Red Cod
Figure 6. Pseudophycis bachus. A, B, NMNZ P.054828, neotype, 351 mm SL, 2.5 km off coast from Whanganui River bar, Whanganui, New Zealand, fresh specimen, lateral view of body and anterior body showing black pectoral blotch respectively (photographs C. Struthers, NMNZ); C, unpublished line drawing by S. Parkinson of Enchelyopus bachus Forster in Bloch and Schneider, 1801 (reproduced from Whitehead, 1969: pl. 31).
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