BL Fisher

Brian L. Fisher

C Thomas

David P. Mindell

DP Faith

E Boakes

Georgina M. Mace

H Miller

J Walston

JA Johnson

Jonathan Eisen

Peter Roopnarine

RDM Page

Richard L. Pyle

Roderic D. M. Page

Sean A. Rands

SHM Butchart

T Clark

VS Chavan

PLoS ONE

English

PubMed

Mindell, D.P.

Fisher, B.L.

Roopnarine, P.

Eisen, J.

Mace, G.M.

Page, R.D.M.

Pyle, R.L.

Enlighten: Publications

Aggregating, tagging and integrating biodiversity research

David P Mindell

Brian L Fisher

Georgina M Mace

Roderic D M Page

Richard L Pyle

Directory of Open Access Journals

Aggregating, tagging and integrating biodiversity research.

Crossref

Aggregating, Tagging and Integrating Biodiversity Research

Mindell, DP

Fisher, BL

Roopnarine, P

Eisen, J

Mace, GM

Page, RD

Pyle, RL

UCL Discovery

OverviewAggregating, Tagging and Integrating BiodiversityResearchDavid P. Mindell1*, Brian L. Fisher1, Peter Roopnarine1, Jonathan Eisen2, Georgina M. Mace3,Roderic D. M. Page4, Richard L. Pyle51California Academy of Sciences, San Francisco, California, United States of America, 2Department of Medical Microbiology, Section of Evolution and Ecology, Universityof California Davis, Davis, California, United States of America, 3Division of Biology, Imperial College London, London, United Kingdom, 4University of Glasgow, Instituteof Biodiversity, Animal Health and Comparative Medicine, Glasgow, United Kingdom, 5Department of Natural Sciences, Bishop Museum, Honolulu, Hawaii, United Statesof AmericaScientists are amassing details about thescope and status of life’s variation at anaccelerating rate. This aids our under-standing of species’ distributions and theirinteractions over space and time. If we areto address the consequences of globalenvironmental change for life’s future,however, biodiversity data must be aggre-gated, integrated and synthesized to amuch greater degree than they are atpresent. Here, we call attention to a newcommunity resource and tool which pro-vides a step in the right direction.PLoS has launched a Biodiversity Hub,http://hubs.plos.org/web/biodiversity/ .aiming to accelerate the discovery, dissem-ination and integration of biodiversitystudies. Biodiversity is broadly construedas life’s variation, including the richness,relationships, functions and distribution ofgenes, species, communities, and ecosys-tems across terrestrial, marine and fresh-water realms. Biodiversity studies oftenintegrate evolution, ecology and conserva-tion science to better understand andconserve life’s variation.The Biodiversity Hub provides threegeneral services. First, the Hub builds onthe idea of open access publication byaggregating selected open access journalarticles focused on biodiversity science.Second, the Hub adds value to previouslypublished content. Initially, that value willinvolve links to images, distribution maps,publications and data about species fea-tured in the articles. Eventually, we hopethe Hub will integrate the semantic mark-up of taxonomic and other biodiversityscience elements within open-access pa-pers. Thus, papers aggregated by the Hubcan include digital images, maps, and datathat are not shown in the originalpublication, and semantically tagged ele-ments (e.g., species names) that can makesuch information much easier to find andsynthesize. We are hopeful that this willimprove professional and public access tobiodiversity data, allowing broader use ofthe information in research and raisingpublic awareness of biodiversity issues.Third, the Hub provides a communityforum for interaction around specificcontent. Commentary and links to re-search resources and community projectscan attract users and broaden support forbiodiversity initiatives. The Hub can bringbiodiversity publications to life.Over the past decade, there has beenconsiderable progress in synthesizing anddigitizing biodiversity-related assets. Resourceassets include aggregated specimen data:GBIF (,http://www.gbif.org/.), The Paleo-biology Database (,http://www.paleodb.org.); interoperability among datasetsand databases: GEO BON (,http://www.earthobservations.org/geobon.shtml.), Glob-al Names Architecture (,http://globalnames.org.); taxonomic literature: BHL (,http://www.biodiversitylibrary.org/.); taxonomicnames: Zoobank (,http://www.zoobank.org/.), IPNI (http://www.ipni.org/), Catalogueof Life (,http://www.catalogueoflife.org.),Index Fungorum (,http://www.indexfun-gorum.org/.); molecular sequence data:GenBank (,http://www.ncbi.nlm.nih.gov/Genbank/.), Barcode of Life (,http://www.dnabarcodes.org/.), Greengenes (,http://greengenes.lbl.gov.); images: MorphBank(,http://www.morphbank.net/.), ARKive(,http://arkive.org/.); phylogenetic rela-tionships: Tree of Life (,http://tolweb.org/tree/.), TreeBASE (,http://www.treebase.org.); natural history: Encyclopedia of Life(,http://www.eol.org/.); conservation sta-tus of species: IUCN Red List (,http://www.iucnredlist.org/.),WWFWildfinder (,http://gis.wwfus.org/wildfinder/.); and ecologi-cal and evolutionary datasets (,http://datadryad.org/.).A lack of integration of these and similarassets, with each other and with thepublication process, limits a realization oftheir full potential. Integrating biodiversityresources depends on linking datasets toanalyses, using shared global identifiers,and deploying services that link thoseidentifiers [1], [2]. These steps and otherscan enhance access and stability over timefor the units of analyses, such as individualmuseum specimens, taxon names, geo-graphic locations, and molecular sequenc-es. Integration of such basic biodiversityelements in publications can result ingreater credit going to the investigatorsand providers of these scientific data. Thecurrent lack of attribution for the continu-ing use of hard-won, primary biodiversitydata (e.g., species descriptions, characterdata sets for phylogenetic analyses, long-term field study observations, curation ofbiodiversity databases) leads universitiesand funding agencies to underestimate thevalue of biodiversity-related disciplines.The integration of assets and openaccess to them can help to change thissituation [3]. For a summary of princi-ples of knowledge-sharing for the Conser-vation Commons and biodiversity data,see http://www.conservationcommons.net/.The PLoS Biodiversity Hub offers a chanceto address some of these shortcomingsand opportunities in the publication processand subsequent use of the literature, whileCitation: Mindell DP, Fisher BL, Roopnarine P, Eisen J, Mace GM, et al. (2011) Aggregating, Tagging andIntegrating Biodiversity Research. PLoS ONE 6(8): e19491. doi:10.1371/journal.pone.0019491Editor: Sean A. Rands, University of Bristol, United KingdomReceived November 8, 2010; Accepted April 7, 2011; Published August 1, 2011Copyright:  2011 Mindell et al. This is an open-access article distributed under the terms of the CreativeCommons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium,provided the original author and source are credited.Funding: The authors have no support or funding to report.Competing Interests: D. Mindell is a member of the steering committee for the PLoS Biodiversity Hub.* E-mail: dmindell@calacademy.orgPLoS ONE | www.plosone.org 1 August 2011 | Volume 6 | Issue 8 | e19491simultaneously enhancing PLoS’s overall mis-sion to disseminate, synthesize, and connectscientific knowledge (see [4], [5]).The most basic challenges for biodi-versity scientists are the more thoroughdescription and comprehension of life’svariation. Providing names and phyloge-netic classifications, where possible, is anintegral part of this task. Current prog-ress in the cataloging of species richnesscan be summarized as follows. Roughly1.7 million species of multi-cellularorganisms have been described andrecognized, including about 62,000 ver-tebrates, 1,300,000 invertebrates,321,000 plants and 51,500 fungi andbrown algae [6]. Diversity and numbersof single-celled life forms including pro-tists, Bacteria, Archaea, and viruses areless extensively described and cannot inmany or most cases be tallied in the sameway due to asexual reproduction, fre-quent lateral gene transfer and differingspecies concepts. The total number ofextant species on Earth is not known,though recent estimates range from 5 to30 million [7], with the most plausibleestimates lying near the lower end of therange. Thus, we may have describedbetween 5.7% to 34% of species with astrong bias to the macrofauna and flora.Taxonomic discovery is not complete forany of the major groups; however, thegaps in our knowledge are particularlyacute for insects, fungi, algae and un-known legions of single-celled organisms.Efforts to bridge these gaps should be apriority, as these poorly known groupsare important components of healthy,functional ecosystems, and play key rolesin nutrient cycling, decomposition, polli-nation, symbioses, and soil fertility, andas primary producers and consumers.Biases exist also on the basis of habitatand environment, with deep ocean anddeep earth environments being poorlyknown relative to more accessible areas.Similarly, the diversity of small life formsliving in or on other species is greatlyunder-sampled. Documenting the num-bers of species and their biotic interac-tions are fundamental to understandingthe complexity, robustness and function-ing of the ecosystems comprising thosespecies.Museum specimen and species data-bases useful for macroorganism researchare growing and becoming more widelyaccessible. Despite the emergence ofother sources of species information inrecent decades, museum data still repre-sent an unparalleled source of broad-based historical information on species[8]. Increasingly, museum databases in-corporate digital images, GIS data, maps,mensural data, and links to speciesdescriptions and other natural historyreferences. Comparative molecular datasets from diverse species also continue togrow, and are providing our best under-standing of microorganism diversity andevolution. An estimate from the GenomesOnLine Database (GOLD; ,http://www.genomesonline.org/.) in March 2011 ofthe number of genome projects complet-ed and in progress includes 5,843 Bacte-ria, 2,003 Eukarya species and 210Archaea. In many cases, annotations ofgene and character homology relation-ships and the structure and function ofgenes and proteins are improving, thoughmuch work is needed in this area.Although our basic knowledge of biodi-versity is increasing, analyses based on thebest available long-term data sets indicatethat the high rates of decline in diversityfor many organismal groups continueundiminished [9]. Estimates of the extinc-tion risks for animals, plants and fungi areaccelerating while negative pressures ex-erted on those species are increasing,including climate change impacts, habitatdestruction, unsustainable exploitation,spread of invasive species and ongoinghuman consumption and competition fornatural resources.The reality of species loss and changingdistributions resulting from human activ-ities lends urgency to the study of connec-tions between the health of biologicaldiversity, the health of ecosystems andultimately the health of human popula-tions. The connections linking biologicaldiversity and human well-being are tradi-tionally discussed in terms of ecosystemsservices. These include the many benefitsthat people derive from nature, such aspotable water, productive soils and nutri-tious food; regulation of climate andinfectious diseases; provision of medicinaland genetic resources; and impacts onquality of life [10], [11]. Adding anevolutionary perspective to these linkageshas been proposed recently with use of theterm ‘‘evosystem services’’ [12]. Thisexplicitly recognizes the value of evolu-tionary processes in generating and main-taining biodiversity and its many valuableproducts.The Biodiversity Hub is a work inprogress. The site is maintained by PLoSstaff working with Hub curators and asteering committee. Current technicallimitations include being restricted toopen access articles indexed by PubMedCentral and not having mechanisms forquickly adding articles or for semantictagging of species names. At present, thearticles aggregated by the BiodiversityHub are not sorted in any way, and wethink that restructuring the site to includetaxonomic and conceptual or methodo-logical section headings could provide anintuitive, meaningful entry point to thelarge set of publications. There is a needfor development of efficient web tools foraggregating and curating articles, and fortagging species names and linking themto relevant sources. The latter tasks areparticularly challenging, given the manygaps in our knowledge of species diversityand the incomplete nature of speciesnames databases. Ideally, the Hub couldbe maintained and curated by thecommunity of biodiversity scientists with-out requiring extensive resources fromPLoS.At present, the site includes a series ofpreviously published, open access biodi-versity articles selected by Hub curators.This includes several articles in whichspecies names have been semanticallytagged by hand, to illustrate the potentialbenefits of semantic tagging and of linkingautomatically to various databases, mapsand unique global identifiers. Interestedreaders should follow links to thesepublications on the Biodiversity Hub andexplore the tagged species names: Fisherand Smith 2008 ,hubs.plos.org/web/biodiversity/article/10.1371/journal.pone.0001787. [13], Walston et al. 2010,hubs.plos.org/web/biodiversity/article/10.1371/journal.pbio.1000485. [14], and Johnsonet al. 2006,hubs.plos.org/web/biodiversity/article/10.1186/1471-2148-6-65. [15].This attempt at automated synthesis forsome biodiversity data is far from com-prehensive, and shows how much workremains to be done. However, extendingsuch efforts to integrate biodiversityknowledge will enhance information ex-change, raise awareness of the great valueof primary biodiversity data, improveattribution of credit for species discoveryand taxonomy, and facilitate syntheses ofthe causes and consequences of globalbiodiversity change. These may, in turn,lead to better understanding of the ways inwhich humans can manage and adapt to achanging world.Author ContributionsWrote the paper: DPM BLF PR JE GMMRDMP RLP.Integrating Biodiversity ResearchPLoS ONE | www.plosone.org 2 August 2011 | Volume 6 | Issue 8 | e19491References1. Clark T, Martin S, Liefeld T (2004) Globallydistributed object identification for biologicalknowledgebases. Brief Bioinform 50: 59–70.2. Page RDM (2008) Biodiversity informatics: thechallenge of linking data and the role of sharedidentifiers. Brief Bioinform 9: 345–354.3. Chavan VS, Ingwersen P (2009) Towards a datapublishing framework for primary biodiversitydata: challenges and potentials for the biodiversityinformatics community. BMC Bioinformatics2009, 10(Suppl. 14): S2.4. Miller H, Norton CN, Sarkar IN (2009) GenBankand PubMed: How connected are they? BMCRes Notes 2: 101.5. Thomas C (2009) Biodiversity databases spread,prompting unification call. Science 324:1632–1633.6. IUCN (2010) IUCN Red List of ThreatenedSpecies. Version 2010.4. Available: http://www.iucnredlist.org. Accessed 2011 May 8.7. Millennium Ecosystem Assessment (2005) Eco-systems and human well-being: biodiversitysynthesis. World Resources Institute, Washington,D.C.8. Boakes E, McGowan PJK, Fuller RA, Chang-qing D, Clark NE, et al. (2010) Distorted views ofbiodiversity: spatial and temporal bias in speciesoccurrence data. PLoS Biol 8: 1–11.9. Butchart SHM, Walpole M, Collen B, vanStrien A, Scharlemann JPW, et al. (2010) Globalbiodiversity: indicators of recent declines. Science328: 1164–1168.10. Naeem S, Bunder DE, Hector A, Loreau M,Perrings C, eds (2009) Biodiversity, ecosystem func-tioning, and human wellbeing: an ecological and economicperspective. Oxford University Press, Oxford.11. Sala OE, Meyerson LA, Parmesan C, eds (2010)Biodiversity change and human health: from ecosystemservices to spread of disease. Island Press, Washington,D.C.12. Faith DP, Magallo´n S, Hendry AP, Conti E,Yahara T, et al. (2010) Evosystem services: anevolutionary perspective on the links betweenbiodiversity and human well-being. Curr OpinEnviron Sustain 2010 2: 66–74.13. Fisher BL, Smith MA (2008) A revision ofMalagasy species of Anochetus Mayr and Odonto-machus Latreille (Hymenoptera: Formicidae).PLoS One 3(5): e1787.14. Walston J, Robinson JG, Bennett EL,Breitenmoser U, da Fonseca GAB, et al. (2010)Bringing the tiger back from the brink —The sixpercent solution. PLoS Biol 8(9): e1000485.15. Johnson JA, Lerner HRL, Rasmussen PC,Mindell DP (2006) Systematics within Gypsvultures: a clade at risk. BMC Evol Biol 6: 65.Integrating Biodiversity ResearchPLoS ONE | www.plosone.org 3 August 2011 | Volume 6 | Issue 8 | e19491

Enlighten

       Mindell, D.P., Fisher, B.L., Roopnarine, P., Eisen, J., Mace, G.M., Page, R.D.M. and Pyle, R.L. (2011) Aggregating, tagging and integrating biodiversity research. PLoS ONE, 6 (8). e19491. ISSN 1932-6203  http://eprints.gla.ac.uk/57032  Deposited on: 16 December 2011   Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk OverviewAggregating, Tagging and Integrating BiodiversityResearchDavid P. Mindell1*, Brian L. Fisher1, Peter Roopnarine1, Jonathan Eisen2, Georgina M. Mace3,Roderic D. M. Page4, Richard L. Pyle51California Academy of Sciences, San Francisco, California, United States of America, 2Department of Medical Microbiology, Section of Evolution and Ecology, Universityof California Davis, Davis, California, United States of America, 3Division of Biology, Imperial College London, London, United Kingdom, 4University of Glasgow, Instituteof Biodiversity, Animal Health and Comparative Medicine, Glasgow, United Kingdom, 5Department of Natural Sciences, Bishop Museum, Honolulu, Hawaii, United Statesof AmericaScientists are amassing details about thescope and status of life’s variation at anaccelerating rate. This aids our under-standing of species’ distributions and theirinteractions over space and time. If we areto address the consequences of globalenvironmental change for life’s future,however, biodiversity data must be aggre-gated, integrated and synthesized to amuch greater degree than they are atpresent. Here, we call attention to a newcommunity resource and tool which pro-vides a step in the right direction.PLoS has launched a Biodiversity Hub,http://hubs.plos.org/web/biodiversity/ .aiming to accelerate the discovery, dissem-ination and integration of biodiversitystudies. Biodiversity is broadly construedas life’s variation, including the richness,relationships, functions and distribution ofgenes, species, communities, and ecosys-tems across terrestrial, marine and fresh-water realms. Biodiversity studies oftenintegrate evolution, ecology and conserva-tion science to better understand andconserve life’s variation.The Biodiversity Hub provides threegeneral services. First, the Hub builds onthe idea of open access publication byaggregating selected open access journalarticles focused on biodiversity science.Second, the Hub adds value to previouslypublished content. Initially, that value willinvolve links to images, distribution maps,publications and data about species fea-tured in the articles. Eventually, we hopethe Hub will integrate the semantic mark-up of taxonomic and other biodiversityscience elements within open-access pa-pers. Thus, papers aggregated by the Hubcan include digital images, maps, and datathat are not shown in the originalpublication, and semantically tagged ele-ments (e.g., species names) that can makesuch information much easier to find andsynthesize. We are hopeful that this willimprove professional and public access tobiodiversity data, allowing broader use ofthe information in research and raisingpublic awareness of biodiversity issues.Third, the Hub provides a communityforum for interaction around specificcontent. Commentary and links to re-search resources and community projectscan attract users and broaden support forbiodiversity initiatives. The Hub can bringbiodiversity publications to life.Over the past decade, there has beenconsiderable progress in synthesizing anddigitizing biodiversity-related assets. Resourceassets include aggregated specimen data:GBIF (,http://www.gbif.org/.), The Paleo-biology Database (,http://www.paleodb.org.); interoperability among datasetsand databases: GEO BON (,http://www.earthobservations.org/geobon.shtml.), Glob-al Names Architecture (,http://globalnames.org.); taxonomic literature: BHL (,http://www.biodiversitylibrary.org/.); taxonomicnames: Zoobank (,http://www.zoobank.org/.), IPNI (http://www.ipni.org/), Catalogueof Life (,http://www.catalogueoflife.org.),Index Fungorum (,http://www.indexfun-gorum.org/.); molecular sequence data:GenBank (,http://www.ncbi.nlm.nih.gov/Genbank/.), Barcode of Life (,http://www.dnabarcodes.org/.), Greengenes (,http://greengenes.lbl.gov.); images: MorphBank(,http://www.morphbank.net/.), ARKive(,http://arkive.org/.); phylogenetic rela-tionships: Tree of Life (,http://tolweb.org/tree/.), TreeBASE (,http://www.treebase.org.); natural history: Encyclopedia of Life(,http://www.eol.org/.); conservation sta-tus of species: IUCN Red List (,http://www.iucnredlist.org/.),WWFWildfinder (,http://gis.wwfus.org/wildfinder/.); and ecologi-cal and evolutionary datasets (,http://datadryad.org/.).A lack of integration of these and similarassets, with each other and with thepublication process, limits a realization oftheir full potential. Integrating biodiversityresources depends on linking datasets toanalyses, using shared global identifiers,and deploying services that link thoseidentifiers [1], [2]. These steps and otherscan enhance access and stability over timefor the units of analyses, such as individualmuseum specimens, taxon names, geo-graphic locations, and molecular sequenc-es. Integration of such basic biodiversityelements in publications can result ingreater credit going to the investigatorsand providers of these scientific data. Thecurrent lack of attribution for the continu-ing use of hard-won, primary biodiversitydata (e.g., species descriptions, characterdata sets for phylogenetic analyses, long-term field study observations, curation ofbiodiversity databases) leads universitiesand funding agencies to underestimate thevalue of biodiversity-related disciplines.The integration of assets and openaccess to them can help to change thissituation [3]. For a summary of princi-ples of knowledge-sharing for the Conser-vation Commons and biodiversity data,see http://www.conservationcommons.net/.The PLoS Biodiversity Hub offers a chanceto address some of these shortcomingsand opportunities in the publication processand subsequent use of the literature, whileCitation: Mindell DP, Fisher BL, Roopnarine P, Eisen J, Mace GM, et al. (2011) Aggregating, Tagging andIntegrating Biodiversity Research. PLoS ONE 6(8): e19491. doi:10.1371/journal.pone.0019491Editor: Sean A. Rands, University of Bristol, United KingdomReceived November 8, 2010; Accepted April 7, 2011; Published August 1, 2011Copyright:  2011 Mindell et al. This is an open-access article distributed under the terms of the CreativeCommons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium,provided the original author and source are credited.Funding: The authors have no support or funding to report.Competing Interests: D. Mindell is a member of the steering committee for the PLoS Biodiversity Hub.* E-mail: dmindell@calacademy.orgPLoS ONE | www.plosone.org 1 August 2011 | Volume 6 | Issue 8 | e19491simultaneously enhancing PLoS’s overall mis-sion to disseminate, synthesize, and connectscientific knowledge (see [4], [5]).The most basic challenges for biodi-versity scientists are the more thoroughdescription and comprehension of life’svariation. Providing names and phyloge-netic classifications, where possible, is anintegral part of this task. Current prog-ress in the cataloging of species richnesscan be summarized as follows. Roughly1.7 million species of multi-cellularorganisms have been described andrecognized, including about 62,000 ver-tebrates, 1,300,000 invertebrates,321,000 plants and 51,500 fungi andbrown algae [6]. Diversity and numbersof single-celled life forms including pro-tists, Bacteria, Archaea, and viruses areless extensively described and cannot inmany or most cases be tallied in the sameway due to asexual reproduction, fre-quent lateral gene transfer and differingspecies concepts. The total number ofextant species on Earth is not known,though recent estimates range from 5 to30 million [7], with the most plausibleestimates lying near the lower end of therange. Thus, we may have describedbetween 5.7% to 34% of species with astrong bias to the macrofauna and flora.Taxonomic discovery is not complete forany of the major groups; however, thegaps in our knowledge are particularlyacute for insects, fungi, algae and un-known legions of single-celled organisms.Efforts to bridge these gaps should be apriority, as these poorly known groupsare important components of healthy,functional ecosystems, and play key rolesin nutrient cycling, decomposition, polli-nation, symbioses, and soil fertility, andas primary producers and consumers.Biases exist also on the basis of habitatand environment, with deep ocean anddeep earth environments being poorlyknown relative to more accessible areas.Similarly, the diversity of small life formsliving in or on other species is greatlyunder-sampled. Documenting the num-bers of species and their biotic interac-tions are fundamental to understandingthe complexity, robustness and function-ing of the ecosystems comprising thosespecies.Museum specimen and species data-bases useful for macroorganism researchare growing and becoming more widelyaccessible. Despite the emergence ofother sources of species information inrecent decades, museum data still repre-sent an unparalleled source of broad-based historical information on species[8]. Increasingly, museum databases in-corporate digital images, GIS data, maps,mensural data, and links to speciesdescriptions and other natural historyreferences. Comparative molecular datasets from diverse species also continue togrow, and are providing our best under-standing of microorganism diversity andevolution. An estimate from the GenomesOnLine Database (GOLD; ,http://www.genomesonline.org/.) in March 2011 ofthe number of genome projects complet-ed and in progress includes 5,843 Bacte-ria, 2,003 Eukarya species and 210Archaea. In many cases, annotations ofgene and character homology relation-ships and the structure and function ofgenes and proteins are improving, thoughmuch work is needed in this area.Although our basic knowledge of biodi-versity is increasing, analyses based on thebest available long-term data sets indicatethat the high rates of decline in diversityfor many organismal groups continueundiminished [9]. Estimates of the extinc-tion risks for animals, plants and fungi areaccelerating while negative pressures ex-erted on those species are increasing,including climate change impacts, habitatdestruction, unsustainable exploitation,spread of invasive species and ongoinghuman consumption and competition fornatural resources.The reality of species loss and changingdistributions resulting from human activ-ities lends urgency to the study of connec-tions between the health of biologicaldiversity, the health of ecosystems andultimately the health of human popula-tions. The connections linking biologicaldiversity and human well-being are tradi-tionally discussed in terms of ecosystemsservices. These include the many benefitsthat people derive from nature, such aspotable water, productive soils and nutri-tious food; regulation of climate andinfectious diseases; provision of medicinaland genetic resources; and impacts onquality of life [10], [11]. Adding anevolutionary perspective to these linkageshas been proposed recently with use of theterm ‘‘evosystem services’’ [12]. Thisexplicitly recognizes the value of evolu-tionary processes in generating and main-taining biodiversity and its many valuableproducts.The Biodiversity Hub is a work inprogress. The site is maintained by PLoSstaff working with Hub curators and asteering committee. Current technicallimitations include being restricted toopen access articles indexed by PubMedCentral and not having mechanisms forquickly adding articles or for semantictagging of species names. At present, thearticles aggregated by the BiodiversityHub are not sorted in any way, and wethink that restructuring the site to includetaxonomic and conceptual or methodo-logical section headings could provide anintuitive, meaningful entry point to thelarge set of publications. There is a needfor development of efficient web tools foraggregating and curating articles, and fortagging species names and linking themto relevant sources. The latter tasks areparticularly challenging, given the manygaps in our knowledge of species diversityand the incomplete nature of speciesnames databases. Ideally, the Hub couldbe maintained and curated by thecommunity of biodiversity scientists with-out requiring extensive resources fromPLoS.At present, the site includes a series ofpreviously published, open access biodi-versity articles selected by Hub curators.This includes several articles in whichspecies names have been semanticallytagged by hand, to illustrate the potentialbenefits of semantic tagging and of linkingautomatically to various databases, mapsand unique global identifiers. Interestedreaders should follow links to thesepublications on the Biodiversity Hub andexplore the tagged species names: Fisherand Smith 2008 ,hubs.plos.org/web/biodiversity/article/10.1371/journal.pone.0001787. [13], Walston et al. 2010,hubs.plos.org/web/biodiversity/article/10.1371/journal.pbio.1000485. [14], and Johnsonet al. 2006,hubs.plos.org/web/biodiversity/article/10.1186/1471-2148-6-65. [15].This attempt at automated synthesis forsome biodiversity data is far from com-prehensive, and shows how much workremains to be done. However, extendingsuch efforts to integrate biodiversityknowledge will enhance information ex-change, raise awareness of the great valueof primary biodiversity data, improveattribution of credit for species discoveryand taxonomy, and facilitate syntheses ofthe causes and consequences of globalbiodiversity change. These may, in turn,lead to better understanding of the ways inwhich humans can manage and adapt to achanging world.Author ContributionsWrote the paper: DPM BLF PR JE GMMRDMP RLP.Integrating Biodiversity ResearchPLoS ONE | www.plosone.org 2 August 2011 | Volume 6 | Issue 8 | e19491References1. Clark T, Martin S, Liefeld T (2004) Globallydistributed object identification for biologicalknowledgebases. Brief Bioinform 50: 59–70.2. Page RDM (2008) Biodiversity informatics: thechallenge of linking data and the role of sharedidentifiers. Brief Bioinform 9: 345–354.3. Chavan VS, Ingwersen P (2009) Towards a datapublishing framework for primary biodiversitydata: challenges and potentials for the biodiversityinformatics community. BMC Bioinformatics2009, 10(Suppl. 14): S2.4. Miller H, Norton CN, Sarkar IN (2009) GenBankand PubMed: How connected are they? BMCRes Notes 2: 101.5. Thomas C (2009) Biodiversity databases spread,prompting unification call. Science 324:1632–1633.6. IUCN (2010) IUCN Red List of ThreatenedSpecies. Version 2010.4. Available: http://www.iucnredlist.org. Accessed 2011 May 8.7. Millennium Ecosystem Assessment (2005) Eco-systems and human well-being: biodiversitysynthesis. World Resources Institute, Washington,D.C.8. Boakes E, McGowan PJK, Fuller RA, Chang-qing D, Clark NE, et al. (2010) Distorted views ofbiodiversity: spatial and temporal bias in speciesoccurrence data. PLoS Biol 8: 1–11.9. Butchart SHM, Walpole M, Collen B, vanStrien A, Scharlemann JPW, et al. (2010) Globalbiodiversity: indicators of recent declines. Science328: 1164–1168.10. Naeem S, Bunder DE, Hector A, Loreau M,Perrings C, eds (2009) Biodiversity, ecosystem func-tioning, and human wellbeing: an ecological and economicperspective. Oxford University Press, Oxford.11. Sala OE, Meyerson LA, Parmesan C, eds (2010)Biodiversity change and human health: from ecosystemservices to spread of disease. Island Press, Washington,D.C.12. Faith DP, Magallo´n S, Hendry AP, Conti E,Yahara T, et al. (2010) Evosystem services: anevolutionary perspective on the links betweenbiodiversity and human well-being. Curr OpinEnviron Sustain 2010 2: 66–74.13. Fisher BL, Smith MA (2008) A revision ofMalagasy species of Anochetus Mayr and Odonto-machus Latreille (Hymenoptera: Formicidae).PLoS One 3(5): e1787.14. Walston J, Robinson JG, Bennett EL,Breitenmoser U, da Fonseca GAB, et al. (2010)Bringing the tiger back from the brink —The sixpercent solution. PLoS Biol 8(9): e1000485.15. Johnson JA, Lerner HRL, Rasmussen PC,Mindell DP (2006) Systematics within Gypsvultures: a clade at risk. BMC Evol Biol 6: 65.Integrating Biodiversity ResearchPLoS ONE | www.plosone.org 3 August 2011 | Volume 6 | Issue 8 | e19491

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