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Pinnotheres atrinicola Roderic D. M. Page 1983, n.sp.
No full textPinnotheres atrinicola n.sp. (Fig. 21,J, 3) Pinnotheres novaezelandiae Filhol. -*Chilton, 1911: 295 296. - Scott, 1961: 307 (part). -Bennett, 1964: 76-79 (part; not figs). - Takeda & Miyake, 1969: 18D-181. Pinnotheres schauinslandi Lenz. -Bennett, 1964: 79-80 (part; not fig. 87 and 89-91). *The original synonym is misspelt in this reference Pinnotheres. Waite, 1909: 52. Pinnotheres "undescribed species". Gordon, 1936: 165. Pinnotheres sp. ("probably P. schauinslandi"). Wear, 1965: 16, 18. Diagnosis. Hard-stage: chelae with a continuous dorsal row of setae on propodus; terminal segment of abdomen quadrate; male 1st pleopod slender, strongly curved in distal third, less setose than in P. novaezelandiae. Mature female: legs noticeably asymmetric; 2nd leg with dactylus subequal to carpus or longer, propodus longer than carpus. First 3 legs with long setae on carpus, propodus, and dactylus. First-stage zoe a larger than in P. novaezelandiae, and with a different chromatophore pattern. Description. Similar to P. novaezelandiae, against which characters are compared. HARD-STAGE (Fig. 3 A-G). Carapace (Fig. 3A) less dorsally inflated, less shouldered, 4.1--8.0 rom wide; front more protruding and convex. Third maxilliped (Fig. 3B) slightly narrower. Chelae (Fig. 3C,D) stouter, less inflated in male than female; row of setae on inner dorsal face of propodus extending from articulation with carpus to articulation with moving finger. Legs with all setae usually more strongly developed and less reduced in large males. Male abdomen (Fig. 3E) with segments 1-3 broader, terminal segment quadrate. Female abdomen (Fig. 3F) broad, convex ventrally, tapering strongly to quadrate terminal segment. Male 1st pleopod (Fig. 3G) less setose, slender, strongly curved laterally in distal third. Colour pattern typically with a large, orange marking along midline of posterior half of carapace. MATURE FEMALE (Fig. 3 H-J). Carapace (Fig. 3H) more laterally inflated and more rounded, less arched longitudinally, less convex dorsally, 10.0 19.9 rom wide. Third maxilliped (Fig. 31) slightly narrower than in hard-stage, Cheliped merus with dorsal setae reduced or absent, ventral row absent; chelae stout, inflated. Legs slender, subcylindrical, the 2nd longest, the 3rd subequal in length to it, the 4th shortest. Second leg (Fig. 3J) with propodus longer than carpus (ratio 1:1.48 ± 0.12 SD; n = 24), dactylus subequal to carpus or longer. Legs noticeably asymmetric (ratio of sum of lengths of last 3 segments of 2nd leg, shortest to longest, 1:1.7 ± 0.07 SD; n = 22); legs on 'shorter' side less robust and setose than those on 'longer' side. Merus with dorsal row of setae extending only halfway along margin. First 3 legs with scattered setae on lower half of merus and carpus, long setae on carpus, propodus, and dactylus. Last leg with scattered setae on dactylus and distal ventral margin of propodus. Abdomen as in P. novaezelandiae. Usually unpigmented. FIRST-STAGE ZOEA (Fig. 21) larger - mean carapace length 0.56 mm (range 0.53-0.63 mm), mean width 0.39 mm (range 0.37-0.43 mm). Rostrum usually shorter. Mandible with incisor process variable, usually bearing 1 major tooth and 4 smaller accessory teeth (Fig. 2J). Chromatophore pattern (Fig. 21; Table 1): lateral carapacial chromatophore with 2, sometimes 3 centres; abdomen with paired black and yellow chromatophores; black subintestinal chromatophores of telson immediately ventral to yellow lateral intestinal chromatophores. Type data. Holotype'; (hard-stage): NEW ZEALAND, Whangarei Harbour between High Island and mainland, 0-1 m, from Atrina zelandica, 13 May 1982, B. Dobson, G. Miles, C. Turbott, and C. Worthington (National Museum of New Zealand, Cr. 3021). Paratypes (National Museum of New Zealand). Bay of Plenty, B. L. Godfriaux, 3 S?, 7'; (sample no. 39A; Cr. 2529). B.S. 488, 40 009.5'S, 174°36'E, c. 18 miles S of Waitotara R. mouth, in 82 m, 2 Mar 1976, LV. Acheron, 1 S? (Cr. 2521). Evans Bay powerhouse intake, 13 Oct 1954, R. K. Dell, 1 S? (Pinnotheres novaezelandiae det. M. Scott, 1959; CL 952). Lyall Bay, Wellington, from A. zelandica, Sep 1949, R. K. Dell, 1 S? (P. novaezelandiae det. M. Scott, 1959; Cr. 955). B.S. 528, 40 036.5'S, 173°oo.5'E, off shelf flats inside Farewell Spit (Tasman Bank), in 24-26 m, 9 Mar 1976, r.v. Acheron, 2 <;? (CL 2519, 2520). B.S. 527, 40 037'S, 172°48'E, c. 5 miles off Pakawau Beach, Golden Bay, in 24 m, 9 Mar 1976, r.v, Acheron, 19<;? (P. novaezelandiae det. G. R. F. Hicks, in A. zelandica; Cr. 2524). 40OJ3'S, 173OZ7'E, in 73 m, from Modiolus areolatus, 10 Apr 1964, r.v. Constantia, 1 <;? (pres. N.Z. Marine Department; Cr. 2528). B.S. 431, Orchard Bay, Marlborough Sounds, from head to entrance, 16 fm, 30 Aug 1975, LV. Acheron, 1 <;? (Cr. 2522). B.S. 515 (41OOO.5'S, 174°oo'E), W side of Forsyth Bay, Marlborough Sounds, in 9-18 m, 5 Mar 1976, r.v, Acheron, 1 <;?, 3gS? (Cr. 2518). Off Cape Campbell, 40 fm, 5 Dec 1956, F. Abernethy, 1 <;? (P. novaezelandiae det. M. Scott, 1959; Cr. 956). Off Cape Campbell, 40 fm, from A. zelandica, Mar 1957, F. Abernethy, 1 <;? (P. novaezelandiae det. M. Scott, 1959; Z. Cr. 687). Off Otago Harbour, from A. zelandica, 9 Mar 1952, vessel Taiaroa, J. C. Yaldwyn, IgS? (Cr. 941). Other material examined. AUTHOR'S PERSONAL COLLEC TION. Whangarei Harbour: same data as holotype, from 86 A. zelandica, 48 2, 28g 2, 50; MacDonald Bank, from A. zelandica, 10 May 1982, 52. Ngataringa Bay, Waitemata Harbour, from A. zelandica, 12 Dec 1981, 42, 2g2, 14 Dec 1981, 112, 4g2, 20, 13 Jan 1982, 92, 2g2, 27 Feb 1982,12,lg2. UNIVERSITY OF AUCKLAND DEPARTMENT OF ZOOLOGY. Okahu Bay, Waitemata Harbour, from Chione stutchburyi, 15 Aug 1981, A. Grimm, 10. AUCKLAND INSTITUTE AND MUSEUM. Ruakaka, Marsden Pt, 2 Jan 1969, W. Farley, 12 (AIM. 3929). J. B. JONES PERSONAL COLLECTION. Seatoun beach, from A. zelandica, 1 2. CANTERBURY MUSEUM. Takapuna Beach, from A. zelandica, 29 Sep 1914, 22 (P. novaezelandiae del. E. W. Bennett, 18 Nov 1930; AQ 2369). Cheltenham Beach, from A. zelandica (ex Chilton Coli., no. 489), 22 (P. schauinslandi det. E. W. Bennett, 18 Nov 1930), 10 (P. novaezelandiae det. E. W. Bennett, 18 Nov 1930; AQ 2383). Auckland (dredged), Capt. Bollons, 22 (P. novaezelandiae det. E. W. Bennett, 18 Nov 1930; AQ 2396). OffLyttelton heads, trawled sand-mud, 25-28 fm, 7 Mar 1967, vessel Golden Light, Mr Smith, 12 (AQ 2066). Nora Niven Expdn 1907, Stations 20 and 44, 52 (AQ 2242). Distribution. North and South islands. Intertidal to 200 m. Endemic. Hosts. The principal host is Atrina zelandica. There are single records of hard-stages from Modiolus areolatus (Gould) and Chione stutchburyi. Waite (1909, p. 52) found that "almost every adult Pinna [= Atrina] taken had its crustacean commensual, Pinnotheres ", as did Stead (1971): in a sample of 87 A. zelandica taken from Whangarei Harbour on 13 May 1982, 83 (95.4%) contained a specimen of P. atrinicola. Remarks. Differences between P. novaezelandiae and Pinnotheres from Atrina zelandica were first noted by Bennett (1964, p. 76), who observed that mature females of "P. novaezelandiae" from A. zelandica were usually larger and had relatively longer legs. Wear (1965) reported zoea larvae of 2 species of Pinnotheres in Wellington Harbour plankton: one he could not distinguish from P. novaezelandiae as described by Bennett (1964, p. 78-79, fig. 92 and 93); the other, he suggested, was probably P. schauinslandi, "as this is the only other adult of the genus Pinnotheres recorded from New Zealand (Bennett, 1964)". Apart from figuring the telson of P. novaezelandiae, Wear did not describe his specimens. Jones (1977) has confirmed that they belong to different species. Using scanning electron microscopy, Jones (1975) compared first-stage zoeae of P. novaezelandiae and Pinnotheres from A. zelandica, noting small differences in the morphology of the rostrum, labrum, and mandibles which led him to suggest that the latter was a different species (Jones 1975, 1978). P. atrinicola is obviously very similar morphologically to P. novaezelandiae. The latter is more common in mytilids, especially Perna canaliculus, while with 2 exceptions P. atrinicola is known only from A. zelandica. Chione stutchburyi is the only host the 2 species have in common. This relative lack of overlap in hosts raises the possibility that the crabs I have recognised here as distinct species are in reality morphs of a single, polymorphic species in which post-planktonic morphology is determined by the identity of the host occupied. However, the morphology of both species is relatively constant, and both P. novaezelandiae and P. atrinicola show no patent morphological changes when found in bivalves other than their respective principal hosts, Perna canaliculus and Atrina zelandica. Further work, such as an electrophoretic study of allele frequencies in pea crabs from these 2 hosts, would help remove any remaining doubt about the status of P. atrinicola. The specific epithet is constructed from Atrina, genus of the type host, and -cola (L.), a suffix denoting one who inhabits.Published as part of Roderic D. M. Page, 1983, Description of a new species of Pinnotheres, and redescription of P. novaezelandiae fBrachyura: Pinnotheridae), pp. 151-162 in New Zealand Journal of Zoology 10 on pages 158-161, DOI: 10.1080/03014223.1983.10423904, http://zenodo.org/record/120876
Description of a new species of Pinnotheres, and redescription of P. novaezelandiae fBrachyura: Pinnotheridae)
No full textRoderic D. M. Page (1983): Description of a new species of Pinnotheres, and redescription of P. novaezelandiae fBrachyura: Pinnotheridae). New Zealand Journal of Zoology 10: 151-162, DOI: 10.1080/03014223.1983.1042390
FIg.2 in Description of a new species of Pinnotheres, and redescription of P. novaezelandiae fBrachyura: Pinnotheridae)
No full textFIg.2 First-stage zoea larvae of (A-H) Pinnotheres novaezelandiae and (I,J) P. atrinicola: A,I, lateral view; B, 慮瑥物潾 view; C,J, mandible; D, maxillule; E, maxilla; F, maxilliped 1; G, maxilliped 2; H, abdomen (solid black- black pigment; stippling - yellow pigment; scale lines represent 0.05 mm except for A, B, H, and I, 0.1 mm).Published as part of Roderic D. M. Page, 1983, Description of a new species of Pinnotheres, and redescription of P. novaezelandiae fBrachyura: Pinnotheridae), pp. 151-162 in New Zealand Journal of Zoology 10 on page 156, DOI: 10.1080/03014223.1983.10423904, http://zenodo.org/record/120876
Fig. 1 in Description of a new species of Pinnotheres, and redescription of P. novaezelandiae fBrachyura: Pinnotheridae)
No full textFig. 1 Pinnorheres novaeulandiae: A, hard-stage 0, dorsal view; B, left 3rd maxilliped, hard-stage 6; C,D, left chela, hard-stage 0, outer and inner faces; E, abdomen, hard-stage 0, ventral view; F, abdomen, hard-stage 9, ventral view; G, left 1st pleopod, 0, sternal view; H, mature 9, dorsal view; I, left 3rd maxilliped, mature'?; J, right 2nd leg, mature 9, anterior view (scale lines represent 1 mm except for A and H, 5 mm).Published as part of Roderic D. M. Page, 1983, Description of a new species of Pinnotheres, and redescription of P. novaezelandiae fBrachyura: Pinnotheridae), pp. 151-162 in New Zealand Journal of Zoology 10 on page 154, DOI: 10.1080/03014223.1983.10423904, http://zenodo.org/record/120876
Pinnotheres atrinicola Page 2012, n.sp.
No full textPinnotheres atrinicola n.sp. (Fig. 21,J, 3) Pinnotheres novaezelandiae Filhol. -* Chilton, 1911: 295 296. - Scott, 1961: 307 (part). - Bennett, 1964: 76-79 (part; not figs). - Takeda & Miyake, 1969: 18D-181. Pinnotheres schauinslandi Lenz. - Bennett, 1964: 79-80 (part; not fig. 87 and 89-91). Pinnotheres. Waite, 1909: 52. Pinnotheres " undescribed species". Gordon, 1936: 165. Pinnotheres sp. ("probably P. schauinslandi"). Wear, 1965: 16, 18. Diagnosis. Hard-stage: chelae with a continuous dorsal row of setae on propodus; terminal segment of abdomen quadrate; male 1st pleopod slender, strongly curved in distal third, less setose than in P. novaezelandiae. Mature female: legs noticeably asymmetric; 2nd leg with dactylus subequal to carpus or longer, propodus longer than carpus. First 3 legs with long setae on carpus, propodus, and dactylus. First-stage zoea larger than in P. novaezelandiae, and with a different chromatophore pattern. Description. Similar to P. novaezelandiae, against which characters are compared. HARD-STAGE (Fig. 3 A-G). Carapace (Fig. 3A) less dorsally inflated, less shouldered, 4.1--8.0 rom wide; front more protruding and convex. Third maxilliped (Fig. 3B) slightly narrower. Chelae (Fig. 3C,D) stouter, less inflated in male than female; row of setae on inner dorsal face of propodus extending from articulation with carpus to articulation with moving finger. Legs with all setae usually more strongly developed and less reduced in large males. Male abdomen (Fig. 3E) with segments 1-3 broader, terminal segment quadrate. Female abdomen (Fig. 3F) broad, convex ventrally, tapering strongly to quadrate terminal segment. Male 1st pleopod (Fig. 3G) less setose, slender, strongly curved laterally in distal third. Colour pattern typically with a large, orange marking along midline of posterior half of carapace. MATURE FEMALE (Fig. 3 H-J). Carapace (Fig. 3H) more laterally inflated and more rounded, less arched longitudinally, less convex dorsally, 10.0 19.9 rom wide. Third maxilliped (Fig. 31) slightly narrower than in hard-stage, Cheliped merus with dorsal setae reduced or absent, ventral row absent; chelae stout, inflated. Legs slender, subcylindrical, the 2nd longest, the 3rd subequal in length to it, the 4th shortest. Second leg (Fig. 3J) with propodus longer than carpus (ratio 1:1.48 ± 0.12 SD; n = 24), dactylus subequal to carpus or longer. Legs noticeably asymmetric (ratio of sum of lengths of last 3 segments of 2nd leg, shortest to longest, 1:1.7 ± 0.07 SD; n = 22); legs on 'shorter' side less robust and setose than those on 'longer' side. Merus with dorsal row of setae extending only halfway along margin. First 3 legs with scattered setae on lower half of merus and carpus, long setae on carpus, propodus, and dactylus. Last leg with scattered setae on dactylus and distal ventral margin of propodus. *The original synonym is misspelt in this reference Abdomen as in P. novaezelandiae. Usually unpigmented. FIRST-STAGE ZOEA (Fig. 21) larger - mean carapace length 0.56 mm (range 0.53-0.63 mm), mean width 0.39 mm (range 0.37-0.43 mm). Rostrum usually shorter. Mandible with incisor process variable, usually bearing 1 major tooth and 4 smaller accessory teeth (Fig. 2J). Chromatophore pattern (Fig. 21; Table 1): lateral carapacial chromatophore with 2, sometimes 3 centres; abdomen with paired black and yellow chromatophores; black subintestinal chromatophores of telson immediately ventral to yellow lateral intestinal chromatophores. Type data. Holotype'; (hard-stage): NEW ZEA LAND, Whangarei Harbour between High Island and mainland, 0-1 m, from Atrina zelandica, 13 May 1982, B. Dobson, G. Miles, C. Turbott, and C. Worthington (National Museum of New Zealand, Cr. 3021). Paratypes (National Museum of New Zealand). Bay of Plenty, B. L. Godfriaux, 3 S?, 7'; (sample no. 39A; Cr. 2529). B.S. 488, 40 009.5'S, 174°36'E, c. 18 miles S of Waitotara R. mouth, in 82 m, 2 Mar 1976, LV. Acheron, 1 S? (Cr. 2521). Evans Bay powerhouse intake, 13 Oct 1954, R. K. Dell, 1 S? (Pinnotheres novaezelandiae det. M. Scott, 1959; CL 952). Lyall Bay, Wellington, from A. zelandica, Sep 1949, R. K. Dell, 1 S? (P. novaezelandiae det. M. Scott, 1959; Cr. 955). B.S. 528, 40 036.5'S, 173°oo.5'E, off shelf flats inside Farewell Spit (Tasman Bank), in 24-26 m, 9 Mar 1976, r.v. Acheron, 2 (CL 2519, 2520). B.S. 527, 40 037'S, <;? 172°48'E, c. 5 miles off Pakawau Beach, Golden Bay, in 24 m, 9 Mar 1976, r.v, Acheron, 19<;? (P. novaezelandiae det. G. R. F. Hicks, in A. zelandica; Cr. 2524). 40OJ3'S, 173OZ7'E, in 73 m, from Modiolus areolatus, 10 Apr 1964, r.v. Constantia, 1 <;? (pres. N.Z. Marine Department; Cr. 2528). B.S. 431, Orchard Bay, Marlborough Sounds, from head to entrance, 16 fm, 30 Aug 1975, LV. Acheron, 1 <;? (Cr. 2522). B.S. 515 (41OOO.5'S, 174°oo'E), W side of Forsyth Bay, Marlborough Sounds, in 9-18 m, 5 Mar 1976, r.v, Acheron, 1 <;?, 3gS? (Cr. 2518). Off Cape Campbell, 40 fm, 5 Dec 1956, F. Abernethy, 1 <;? (P. novaezelandiae det. M. Scott, 1959; Cr. 956). Off Cape Campbell, 40 fm, from A. zelandica, Mar 1957, F. Abernethy, 1 <;? (P. novaezelandiae det. M. Scott, 1959; Z. Cr. 687). Off Otago Harbour, from A. zelandica, 9 Mar 1952, vessel Taiaroa, J. C. Yaldwyn, IgS? (Cr. 941). Other material examined. AUTHOR'S PERSONAL COLLEC TION. Whangarei Harbour: same data as holotype, from 86 A. zelandica, 48 2, 28g 2, 50; MacDonald Bank, from A. zelandica, 10 May 1982, 52. Ngataringa Bay, Waitemata Harbour, from A. zelandica, 12 Dec 1981, 42, 2g 2, 14 Dec 1981, 112, 4g 2, 20, 13 Jan 1982, 92, 2g 2, 27 Feb 1982,12,lg2. UNIVERSITY OF AUCKLAND DEPARTMENT OF ZOOLOGY. Okahu Bay, Waitemata Harbour, from Chione stutchburyi, 15 Aug 1981, A. Grimm, 10. AUCKLAND INSTITUTE AND MUSEUM. Ruakaka, Marsden Pt, 2 Jan 1969, W. Farley, 12 (AIM. 3929). J. B. JONES PERSONAL COLLECTION. Seatoun beach, from A. zelandica, 1 2. CANTERBURY MUSEUM. Takapuna Beach, from A. zelandica, 29 Sep 1914, 22 (P. novaezelandiae del. E. W. Bennett, 18 Nov 1930; AQ 2369). Cheltenham Beach, from A. zelandica (ex Chilton Coli., no. 489), 22 (P. schauinslandi det. E. W. Bennett, 18 Nov 1930), 10 (P. novaezelandiae det. E. W. Bennett, 18 Nov 1930; AQ 2383). Auckland (dredged), Capt. Bollons, 22 (P. novaezelandiae det. E. W. Bennett, 18 Nov 1930; AQ 2396). Off Lyttelton heads, trawled sand-mud, 25-28 fm, 7 Mar 1967, vessel Golden Light, Mr Smith, 12 (AQ 2066). Nora Niven Expdn 1907, Stations 20 and 44, 52 (AQ 2242). Distribution. North and South islands. Intertidal to 200 m. Endemic. Hosts. The principal host is Atrina zelandica. There are single records of hard-stages from Modiolus areolatus (Gould) and Chione stutchburyi. Waite (1909, p. 52) found that "almost every adult Pinna [= Atrina] taken had its crustacean commensual, Pinnotheres ", as did Stead (1971): in a sample of 87 A. zelandica taken from Whangarei Harbour on 13 May 1982, 83 (95.4%) contained a specimen of P. atrinicola. Remarks. Differences between P. novaezelandiae and Pinnotheres from Atrina zelandica were first noted by Bennett (1964, p. 76), who observed that mature females of " P. novaezelandiae " from A. zelandica were usually larger and had relatively longer legs. Wear (1965) reported zoea larvae of 2 species of Pinnotheres in Wellington Harbour plankton: one he could not distinguish from P. novaezelandiae as described by Bennett (1964, p. 78-79, fig. 92 and 93); the other, he suggested, was probably P. schauinslandi, "as this is the only other adult of the genus Pinnotheres recorded from New Zealand (Bennett, 1964)". Apart from figuring the telson of P. novaezelandiae, Wear did not describe his specimens. Jones (1977) has confirmed that they belong to different species. Using scanning electron microscopy, Jones (1975) compared first-stage zoeae of P. novaezelandiae and Pinnotheres from A. zelandica, noting small differences in the morphology of the rostrum, labrum, and mandibles which led him to suggest that the latter was a different species (Jones 1975, 1978). P. atrinicola is obviously very similar morphologically to P. novaezelandiae. The latter is more common in mytilids, especially Perna canaliculus, while with 2 exceptions P. atrinicola is known only from A. zelandica. Chione stutchburyi is the only host the 2 species have in common. This relative lack of overlap in hosts raises the possibility that the crabs I have recognised here as distinct species are in reality morphs of a single, polymorphic species in which post-planktonic morphology is determined by the identity of the host occupied. However, the morphology of both species is relatively constant, and both P. novaezelandiae and P. atrinicola show no patent morphological changes when found in bivalves other than their respective principal hosts, Perna canaliculus and Atrina zelandica. Further work, such as an electrophoretic study of allele frequencies in pea crabs from these 2 hosts, would help remove any remaining doubt about the status of P. atrinicola. The specific epithet is constructed from Atrina, genus of the type host, and -cola (L.), a suffix denoting one who inhabits.Published as part of Page, Roderic D. M., 2012, Description of a new species of Pinnotheres, and redescription of P. novaezelandiae (Brachyura: Pinnotheridae), pp. 151-162 in New Zealand Journal of Zoology 10 (2) on pages 158-161, DOI: 10.1080/03014223.1983.1042390
BioGUID: resolving, discovering, and minting identifiers for biodiversity informatics
Get PDF<b>Background</b>: Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs, HTTP URIs, and LSIDs).
<b>Results</b>: BioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers.
<b>Conclusion</b>: BioGUID is available at http://bioguid.info/. Source code is available from http://code.google.com/p/bioguid/
Linking NCBI to Wikipedia: a wiki-based approach
Get PDFThe NCBI Taxonomy underpins many bioinformatics and phyloinformatics databases, but by itself provides limited information on the taxa it contains. One readily available source of information on many taxa is Wikipedia. This paper describes iPhylo Linkout, a Semantic wiki that maps taxa in NCBI's taxonomy database onto corresponding pages in Wikipedia. Storing the mapping in a wiki makes it easy to edit, correct, or otherwise annotate the links between NCBI and Wikipedia. The mapping currently comprises some 53,000 taxa, and is available at http://iphylo.org/linkout. The links between NCBI and Wikipedia are also made available to NCBI users through the NCBI LinkOut service
Strategies for assembling the biodiversity knowledge graph
Get PDFThis talk explores different strategies for assembling the “biodiversity knowledge graph” (Page 2016). The first is a centralised, crowd-sourced approach using Wikidata as the foundation. Wikidata is becoming increasingly attractive as a knowledge graph for the life sciences (Waagmeester et al. 2020), and I will discuss some of its strengths and limitations, particularly as a source of bibliographic and taxonomic information. For example, Wikidata’s handling of taxonomy is somewhat problematic given the lack of clear separation of taxa and their names.
A second approach is to build biodiversity knowledge graphs from scratch, such as OpenBioDiv (Penev et al. 2019) and my own Ozymandias (Page 2019). These approaches use either generalised vocabularies such as schema.org, or domain specific ones such as TaxPub (Catapano 2010) and the Semantic Publishing and Referencing Ontologies (SPAR) (Peroni and Shotton 2018), and to date tend to have restricted focus, whether geographic (e.g., Australian animals in Ozymandias) or temporal (recent taxonomic literature, OpenBioDiv). A growing number of data sources are now using schema.org to describe their data, including ORCID and Zenodo, and efforts to extend schema.org into biology (Bioschemas) suggest we may soon be able to build comprehensive knowledge graphs using just schema.org and its derivatives.
A third approach is not to build an entire knowledge graph, but instead focus on constructing small pieces of the graph tightly linked to supporting evidence, for example via annotations. Annotations are increasingly used to mark up both the biomedical literature (e.g., Kim et al. 2015, Venkatesan et al. 2017) and the biodiversity literature (Batista-Navarro et al. 2017). One could argue that taxonomic databases are essentially lists of annotations (“this name appears in this publication on this page”), which suggests we could link literature projects such as the Biodiversity Heritage Library (BHL) to taxonomic databases via annotations. Given that the International Image Interoperability Framework (IIIF) provides a framework for treating publications themselves as a set of annotations (e.g., page images) upon which other annotations can be added (Zundert 2018), this suggests ways that knowledge graphs could lead directly to visualising the links between taxonomy and the taxonomic literature.
All three approaches will be discussed, accompanied by working examples
Deletion of vitamin D receptor leads to premature emphysema/COPD by increased matrix metalloproteinases and lymphoid aggregates formation
Get PDFDeficiency of vitamin D is associated with accelerated decline in lung function. Vitamin D is a ligand for nuclear hormone vitamin D receptor (VDR), and upon binding it modulates various cellular functions. The level of VDR is reduced in lungs of patients with chronic obstructive pulmonary disease (COPD) which led us to hypothesize that deficiency of VDR leads to significant alterations in lung phenotype that are characteristics of COPD/emphysema associated with increased inflammatory response. We found that VDR knock-out (VDR(-/-)) mice had increased influx of inflammatory cells, phospho-acetylation of nuclear factor-kappaB (NF-κB) associated with increased proinflammatory mediators, and up-regulation of matrix metalloproteinases (MMPs) MMP-2, MMP-9, and MMP-12 in the lung. This was associated with emphysema and decline in lung function associated with lymphoid aggregates formation compared to WT mice. These findings suggest that deficiency of VDR in mouse lung can lead to an early onset of emphysema/COPD because of chronic inflammation, immune dysregulation, and lung destruction
Text-mining BHL: towards new interfaces to the biodiversity literature
Get PDFThe taxonomic literature is one of the largest resources of information on biodiversity, both current and in the past. Unlike many scientific disciplines this literature remains perpetually relevant as successive taxonomic work builds upon those earlier foundations. Projects such as the Biodiversity Heritage Library (BHL) have greatly increased access to that literature, as have numerous independent digitisation efforts by museums, herbaria, and publishers. But the focus of this access has been human readers, with limited use of text mining tools, mostly focussed on extracting taxonomic names. This talk explores other kinds of data that can be extracted from text on BHL and elsewhere, focusing on taxonomic names, geographic localities and specimen codes in the context of the BioStor project (https://biostor.org, Page 2011).
The problem of finding taxonomic names in text has been well studied (e.g., Akella et al. 2012), and new BHL content is continuously indexed by names. Despite this, there is only weak linkage between taxonomic name databases and BHL. Even projects that create these links (e.g., BioNames, Page 2013) do not enable links in the reverse direction. In other words, a BHL reader is unaware whether the appearance of a name on a page is the first publication of that name, nor are they told of the fate of a name in subsequent research. The absence of these links reduces the value of BHL to working taxonomists.
In addition to taxonomic names, a typical taxonomic paper often contains specimen codes. Extracting these from text and linking them to digital representations, such as occurrence records in GBIF, opens up the possibility to provide detailed provenance for occurrence data, as well as citation-based metrics for the utility of natural history collections.
Taxonomic papers are also often rich in geographic information. A simple method for extracting locality information from text is to search for latitude and longitude coordinates, and BioStor currently does this. To date some 83,000 individual point localities have been extracted (Fig. 1 ). These are used to provide a simple geographic search interface in BioStor, and are also harvested by JournalMap (Karl et al. 2013). But these localities are not linked to the original location in the source text, nor are they linked to any associated specimens, so they cannot be interpreted as occurrences that could be harvested by GBIF. If the goal is to contribute to GBIF then we need tools that can parse locality information and link that to associated specimens.
A general framework for handling data on taxonomic names, specimens, and geographic localities in text is to treat them as annotations (Batista-Navarro et al. 2017). By modelling annotations using the Web Annotation Data Model (https://www.w3.org/TR/annotation-model/ ) we can incorporate these annotations into biodiversity knowledge graphs (Page 2016). We can also combine these annotations with new standards for describing digitised content, such as the International Image Interoperability Framework (IIIF, https://iiif.io). The implications of this approach for developing new interfaces to the biodiversity literature will be discussed
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