Knowledge bleed, Phenbank, and Namesfor. Life George M. Garrity, Catherine Lyons & James R. Cole Michigan State University and Namesfor. Life, LLC Funding for this research has been provide by the US Department of Energy, Grants No. DE -FG 02 -04 ER 63933 and DE-FG 02 -99 ER 62848, the National Science Foundation Award No. DBI-0328255 and the Michigan University Commercialization Initiative (MUCI) program. Portions of this work are covered under US and foreign patents (pending) and are the intellectual property of the Michigan State University Board of Trustees. For further information contact garrity@msu. edu FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Rumsfeld’s axiom and knowledge bleed “…because as we know, there are knowns; there are things we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there also unknowns -- the ones we don't know. ” FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Kn kn ow ow n ns s Kn un ow kn n ow n Un kn kn ow ow ns n Un un kn kn ow ow n ns The knowledge gradient Semantic resolution Knowledge bleed Basic and applied provides a mechanism results is a loss of research advances to that has knowledge combat knowledge bleed already been gained FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
We do quagmires FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 Alteromonas macleodii(T) communis vaga FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 Alteromonas macleodii(T) communis vaga haloplanktis FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 1976 Alteromonas macleodii(T) communis vaga haloplanktis rubra FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 1976 1977 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 1976 1977 1978 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 1976 1977 1978 1979 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 1976 1977 1978 1979 1981 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 1976 1977 1978 1979 1981 1982 Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 1976 1977 1978 1979 1981 1982 1984 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Marinomonas communis(T) vaga Nomenclatural issues Homotypic synonymy Priority Rule 37(a) 1 Data issues One to many relationship Taxonomic issue Which one is right? Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Marinomonas communis(T) vaga Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Marinomonas communis(T) vaga Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum Marinomonas communis(T) vaga Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae Nomenclatural issue Non-type strains
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae Nomenclatural issues Heterotypic synonymy Data issue Many to many relationship Taxonomic issue Which one is right?
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae Pseudoalteromonas haloplanktis(T) haloplanktis tetradonis atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea elyakoviii FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae Pseudoalteromonas haloplanktis(T) haloplanktis tetradonis atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga mediterannea Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea elyakoviii FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea Pseudoalteromonas haloplanktis(T) haloplanktis tetradonis atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga mediterannea Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea elyakoviii FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica Pseudoalteromonas haloplanktis(T) haloplanktis tetradonis atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetrodonis
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga mediterannea Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea elyakoviii FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna Pseudoalteromonas haloplanktis(T) haloplanktis tetradonis atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetrodonis
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga mediterannea primoryensis Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea elyakoviii stellipolaris litorea FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna mariniintestina saire schlegeliana gaetbuli 5 others Pseudoalteromonas haloplanktis(T) haloplanktis tetradonis atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetrodonis 12 others
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga mediterannea primoryensis Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea elyakoviii stellipolaris litorea 2 others FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna mariniintestina saire schlegeliana gaetbuli 8 others 2005 Pseudoalteromonas haloplanktis(T) haloplanktis tetradonis atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetrodonis 14 others
1972 1973 1976 1977 1978 1979 1981 1982 1984 1986 1987 1988 1990 1992 1995 1997 2000 2001 2002 2004 2005 Oceanosprillum linum(T) japonicum minutium biejerinckii maris williamsae hiroshimense multiglobiferum pelagicum pusillum commune jannaschii kreigii vagum biejerinckii pelagicum maris hiroshimense Marinomonas communis(T) vaga mediterannea primoryensis Alteromonas macleodii(T) communis vaga haloplanktis rubra citrea esperjiana undina aurantia putrifaciens hanedai luteoviolaceae denitrificans colwelliana tetradonis atlantica carageenovora distincta fuliginea elyakoviii stellipolaris litorea 2 others FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Shewanella putrifaciens(T) benthica hanedai colwelliana algae fridgidimarina geldimarina woodyii amazonensis baltica oneidensis pealeana violacea japonica denitrificans livingstonensis alleyanna mariniintestina saire schlegeliana gaetbuli 13 others 2006 Pseudoalteromonas haloplanktis(T) haloplanktis tetradonis atlantica aurantia carrageenovora citrea esperjiana luteoviolacea nigrifaciens pisicida rubra undina antartica bacteriolytica prydzensis tunicata distincta elyakovii peptidolytica tetrodonis 14 others
Since first being defined The genus Alteromonas has undergone 18 “emendations” 21 species were added to the genus 19 species were reassigned to four genera 3 of which are formed as new combinations of Alteromonas spp. 6 synonyms 2 species reduced to subspecies, then re-elevated to species 50 names, five genera, five families, and two classes but…. only five validly published named species of Alteromonas remain. This is not a very complicated example But wait, there is still more FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
May 2004 November 2004 Gammaproteobacteria Alteromonadales Alteromonadacea Colwelliaceae Alteromonas Colwelliaceae Aestuariibacter Idiomarinaceae Thalassomonas Alishewanella Colwellia Ferrimonas Ferrimonadacea Ferrimonas Glaciecola Idiomarina Marinobacter 1 Family 16 genera -> 8 families 12 genera Marinobacterium 1 unclassified -> 7 unclassfied Which is correct? Microbulbifer Which is supported by the data? Moritella Pseudoalteromonas Psychromonas Shewanella Thalassomonas Incertae sedis Pseudoalteromonadaceae Pseudoalteromonas Algicola Idiomarina Psychromonadaceae Psychromonas Incertae sedis Agarvorans Alishewanella Shewanellaceae Shewanella Moritellaceae Moritella Teredinibacter FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Marinobacterium Microbulbifer Salinomonas Teredinibacter
Nomenclature (the end-user’s perspective) Wouldn’t it be nice if… Biological names were really useful Would link to… Relevant literature Sequences Other phenotypic data Sources of strains in Biological Resource Centers Ancillary materials Patents Laws and regulations Regardless of where the data resides Without having to know anything about Synonymies Orthographic variants Misapplications of the name How could this be accomplished? FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Modeling names and taxa… FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Authority+ Taxon Name+ Species+ Strain+ Sequence+ FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Literature Governing bodies Authority+ Taxon Name+ Species+ Strain+ Collections BRC Sequence+ Gen. Bank DDBJ EMBL others FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Proposals STM Legal General Source+ Literature Governing bodies Priority Validity Synonymy Type Authority+ Databases Name+ Taxon Public Private Species+ Strain+ Feature+ direct indirect Source+ Collections BRC Gen. Bank DDBJ EMBL others FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 GSC Core Phenotype FAME Biolog PA
However, rules are made to be broken… FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Name+ Species+ Strain+ Feature+ A properly formed species Feature+ Candidatus or exemplar lost Name+ Environmental sequence Name+ Species+ Feature+ Species+ Strain+ Old type strain, not yet sequenced “Name”+ Strain* Old type, exemplar based on drawing or description FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Feature+ Misidentified taxon
Differing opinions… Name+ Strain+ Feature+ Taxon Species+ Strain+ Taxon Strain+ Feature+ Homotypic synonymy Feature+ Heterotypic synonymy FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
The impact of “uncontrolled” labeling of environmental sequence and strain data … FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Non-types, clones, environmental sequences ID+ “Name”+ Strain* Feature+ Environmental sequence Feature+ Misidentified taxon FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Top 25 labels on 16 S r. RNA sequences for type strains 1200 n = 15232 unique sequences 2. 74 X over defined 1000 800 600 400 200 FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 B 2 17 16 I 12 14 11 B R 9 C D 10 Ta nz an ia 8 B 7 6 A 5 4 3 1 0
FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
The case of the Verrucomicrobia FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
“Identifiers” on Verrucomicrobia 16 S r. RNA sequences, n=911 FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Publication field from Genbank record, n=627 FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Verrucomicrobia, based on annotation (n=444) Unclassified Victivalalles & Lentisphaeralles Unclassified Xiphinematobact Optitutus Verrucomicrobia Proteobacteria FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Taxonomic structure of the Verrucomicrobia revealed Unclassified Optitutus Verrucomicrobium Chthoniobacter Xiphenematobact Verrucomicrobium Rubritalea Prosthecobacter Verrucomicrobium Akkermansia Lentisphaera FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Accessing the Namesfor. Life information objects FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
How Namesfor. Life disambiguates biological nomenclature FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
The underlying concepts Persistent identifiers A name or an identifier for a resource that uniquely identifies that resource and will be forever associated with that resource. It will never be reassigned to any other resource and will not change regardless of where the resource is located or whatever protocol is used to access it. Use of a well managed persistent identifier rather than a location will ensure that when a document is moved, or its ownership changes, the links to it will remain actionable. From: Diana Dack. 2001. Persistence is a Virtue Information Online Conference, Sydney. FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
The underlying concepts (cont. ) Semantic resolution The process of identifying the precise meaning of terms or concepts and mapping them into different classifications. Static concepts Unaffected by new knowledge Dynamic concepts Affected by new knowledge What’s so important about precise meaning in scientific, technical, or medical fields? …in commerce? FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
The underlying concepts (cont. ) The process of mapping a persistent identifier to a URL that retrieves a resource. The URL locates the named resource identified by the persistent identifier (the name). Name resolution PID Identifies PID 1 PID 2 PID 3 URL 1 URL 2 URL 3 URL Locates Name resolution Resource Adapted from: Name Resolution Service: Introduction and Use, Harvard University Library FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
The underlying concepts (cont. ) Handle The Handle system is a comprehensive system for assigning, managing, and resolving persistent identifiers, known as ‘handles’ for digital objects and other sources on the Internet. Handles can be used as Uniform Resource Names (URNs). Digital object identifiers (DOIs) It is implicit in the Handle design that a digital object has associated metadata (data about data; here: data about the digital object). The core piece of metadata is the Handle itself. FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
doi> URL DOI Assigner DOI URL DOI Content DOI URL DOI directory DOI URL DOI Content DOI URL URLDOI URL FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Courtesy of Norman Paskin, International DOI Foundation
Namesfor. Life What is it? A novel technology An ontology, metadata model, and a mapping A transparent information layer on the Internet An application of persistent identifiers A semantic resolution service for the life sciences What isn’t it? A content provider What is the purpose? Solve a well known problem Ambiguity in terminology Common problem Pervasive in life sciences The special case of biological nomenclature Queries and literature searches Assertions, assumptions, hypotheses FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Why DOIs are the preferred GUID DOIs Digital object identifiers Strengths - opaque, actionable, require metadata, identify an object, strong governance, widespread usage, not based on DNS, guarantee of persistence, proposed ISO standard. Weakness - Not free Technically robust Proven technology DOIs are layered on top of CNRI’s Handle server Scalable Widespread use in publishing industry (Cross. Ref) > 1500 publishers and >1000 libraries subscribing > 22 M DOIs assigned > 11 M click-throughs (2/15/2006 - 3/15/2006) Well understood technology Strong social/legal framework to ensure persistence FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Two components N 4 L architecture Taxon DOI Name Rank Parent name Parent taxon DOI Methodology Members Taxon DOI Name Taxon DOI Name Taxon DOI Name Higher Taxon object A transparent information layer to provide DOI services to the life science community An ontology with a schema that produces metadata consistent with requirements of the International DOI Foundation Seven first class object types Name, Taxon, Exemplar, Nomos, Practitioner, Feature, Nomenclatural Code Taxon DOI Name Rank Parent name Parent taxon DOI Methodology Type exemplar DOI Name status Authority Synonyms Taxon DOI Taxon object Name object FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Exemplar DOI Biodeposit Feature Taxon DOI Species name Exemplar object
Two components (continued) The prototype DOI: 10. 1601/tx. 0 A proof-of-principle application 24, 176 first-class objects Track changes in concepts over time Based on a nomenclatural taxonomy, but capable of supporting multiple taxonomic views and “time travel” Initial DOI services conform to AP 0 Released January 17, 2006 Japanese prototype released June 21, 2006 Chinese version under development Arabic version under consideration FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Easy support of foreign languages FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
The mini-monograph Taxon DOI Name Rank Parent name Parent taxon DOI Methodology Type exemplar DOI Nontype exemplar DOI IJSEM/ICSP Taxonomic authorities BRCs & Collections Genbank/EMBL/DDBJ Taxonomic community Genomics community Instrument vendors Database providers Publishers Name DOI Name status Authority Synonyms Taxon DOI Exemplar DOI Biodeposit Feature Taxon DOI Species name FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Preamble Name/Name DOI Name status, Authority Synonyms/Name DOI Member of: Parent Taxon DOI Methodology Type Exemplar DOI Biodeposit+ Feature+ Paired Sequences Genomic Paired phenotypic data Minimal description GSC Core description Images Nontype exemplar Biodeposit+ Feature+ Paired Sequences Genomic Paired phenotypic data Minimal description GSC Core description Images Reference DOIs
“Test ideas in the marketplace. You learn from hearing a range of perspectives. Consultation helps engender the support decisions need to be successfully implemented. ” FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Two components (continued) N 4 L business Member of the International DOI Foundation Self-supporting model Four target groups End-users - access to N 4 L objects as a DOI service at no-charge Publishers - hosting N 4 L enabled content in which each name becomes actionable. Literature could be traversed based on named entities (organisms, genes, etc). Database providers, instrument vendors, BRCs rely on curated information for their own businesses Registrants who wish to provide data or services that are not readily available to the broader community Service for registration of “not-yet-cultivated” taxa and environmental clones We are soliciting input from the community as well as potential collaborators and “clients” FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Synergistic activities Goals of Namesfor. Life Synchronize usage of nomenclature in databases and elsewhere Establish links between vertically integrated business Help build new relationships Stimulate new business opportunities Build useful new tools and services Become a self-supporting service for the community Collaborators/Partners ATCC - nomenclature support, conduit to new customers for existing goods and services, opportunity for new services (pay-for-view data) Forsyth Research Institute - further testing and refinement of the N 4 L model, creation of minimonographs, extension to nyc and uncultivated species Midi Inc. - Integration of N 4 L services with instrument output, pay-for-view data SGM/ICSP/JC - optimize N 4 L DOI imbedding, custom web tag libraries for on-the-fly updating of content FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Embedding N 4 L links into web content FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Phen. Bank… The federated database Associate phenotypic data with emerging 16 S sequence data Potential value to the community Problems Technical Interoperability and data comparability Variable granularity Lack of controlled vocabulary Social issues of the centralized model Who controls access? Who curates? Who pays? Incentives for participants? FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Phen. Bank… A decade later Maturation of the 16 S data Impact of emerging technologies Large-scale sequencing efforts Wealth of new tools Predictive models Ontology development Phenotypic arrays Rapid emergence of web technologies Impact on traditional publishing XML, DOIs Semantic technology Impact of emerging social trends Community annotation, social tagging Open access and supplementary data Incentives for data sharing Distributed model, data discovery “Pay-for-view” vs. regeneration FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Sequencing the type strains Year 2007 2008 2009 2010 2011 2012 2013 2014 200 300 450 675 1013 1519 2278 3417 Cost/Genome* 20000 13333 8889 5926 3951 2634 1756 1171 Genomes/$5 M Cumulative genomes sequenced 250 376 563 844 1266 1898 2848 4271 250 625 1188 2031 3297 5195 8043 12314 BP per dollar Selection of Targets Type Culture Material JGI Sequencing Rapid Annotation (24 Hours) Database Repository Phenotype Prediction Model Generation Metabolic Reconstruction Source – Rick Stevens, Argonne National Laboratory and University of Chicago FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Thanks to MSU Julia Bell Scott Harrison Judy Leventhal Donna Mc. Garrell Siddique Mohideen Qiong Wang Univ. Michigan Paul Saxman Forsyth Inst. Floyd Dewhirst Midi Inc. Myron Sasser Gary Jackoway ATCC Tim Lilburn DSMZ Brian Tindall University of Toulouse Jean Euzéby IDF Norman Paskin Nexus. Tech. Ventures Todd Zahn NIES Japan Junko Shimura Kaduo Hiraki Questions? FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 Soc. General Microbiology Robin Dunford Ron Fraser Int. Com. System. Prok. Aharon Oren Hans Juergen Busse IJSEM Peter Kaempfer Argonne National Lab Rick Stevens Funding US DOE BER NSF Mich Univ. Comm. Init.
FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Acknowledgements MSU Jim Cole Donna Mc. Garrell AKS Mohideen Qiong Wang Scott Harrison Connie Williams Judy Leventhal Julia Bell Denise Searles VPGR and OIP Funding ATCC Tim Lilburn DSMZ Brian Tindall University of Toulouse Jean Euzaby IDF Norman Paskin Paul M. Hunt Lorraine Hudson FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006 US Department of Energy Office of Science National Science Foundation Michigan University Commercialization Initiative
“I would not say that the future is necessarily less predictable than the past. I think the past was not predictable when it started. " FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Insert statement of problem here FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
"I believe what I said yesterday. I don't know what I said, but I know what I think, and, well, I assume it's what I said. " FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
“Simply because you do not have evidence that something does exist does not mean that you have evidence that it doesn't exist. " FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
"Learn to say 'I don't know. ' If used when appropriate, it will be often. " FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
"If I know the answer I'll tell you the answer, and if I don't, I'll just respond, cleverly. " FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
“I don't do quagmires. ” FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Stan Falkow’s observation “Given a choice, most taxonomists would rather wear each other’s underwear than use each other’s names” Why is this so? FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Consider the following A simple exchange between a customer and vendor of “technical” products Discussions among physicians, healthcare providers, and insurers FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
The name/taxon disjunction Impact Accumulation of dubious names in literature/databases Effects assertions of: Identity, commonality of pathways, common ancestry, homology, parology, xenology Legal consequences FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Problems in print publishing Key requirement Proposals and emendations must appear in print Code specific Prokaryotic Code Effective, legitimate, and valid Registration Taxonomies are retrospective Can only cite earlier publications Cannot cite future emendations Increasingly based on molecular sequence data Deposit of sequence data in public databases Not conveniently referenced in print FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Problems with electronic publishing No formal publishing mechanisms Does not fulfill fundamental requirement of the Code(s) Lack bibliographic information Not citable Not persistent Subject to uncontrolled change May disappear Link rot 404 Link not found FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Problems in nomenclature Systematic biologists Marking territory Personal achievement Everyone else (aka end-users) Unfamiliar with literature Unique aspects Unaware of Codes of Nomenclature Legalistic framework Formation and assignment of names Circumscription and emendation of taxa Priority and citation Synonymy and homonymy Correction of orthographic errors Adjudication of nomenclatural disputes But Do not govern classification or identification FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Problems in nomenclature (cont. ) Systematic biologists Primary entry point into STM literature and databases Prominent role in laws/regulations But… Poor identifiers Fixed in time and scope May not be revised Synonymies generally not address Persist, but obsolesce in relation to taxon An archival record of a taxonomic definition for a single point in time What are the alternatives? FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Summary of identifier properties FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
DOI - Handle relationship The Handle System is one component of the DOI System Global name service Secure name resolution over the Internet and Grid The Digital Object Identifier System DOI System uses the Handle System as part of a value-added application DOIs provide persistent, semantically interoperable identification of IP resources The DOI system provides a ready to use Numbering syntax Resolution service Data model Policies and procedures for implementation Expanded technical infrastructure and features specific to DOI applications FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Persistence is not required No appropriate social structure is provided The Digital Object Identifier System The IDF extends the technical infrastructure of the Handle System by provides a social infrastructure guaranteeing persistence Function of organizations, not technology Federation of Registration Agencies IDF policies ensure DOIs “live” even if RAs fail RAs provide the process of DOI transfer IDF is persistent as it is self-funding DOI System is backed by several major public companies, multiple RAs, and a large customer base FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Consistency Ensures interoperability for resolution purposes across Handle System implementations No requirements for interoperability at the application level The Digital Object Identifier System Adds consistent rules for multiple applications IDF set rules for DOI assignment What DOIs can be applied to Restrictions on arbitrary/temporary assignment Restrictions on removal Management by a Directory Manager to enforce QC DOI API defines consistent way of accessing and managing DOI applications and services Consistent use of DOI prefix and numbering syntax provides numbering interoperability in the IP sector, brand recognition, understanding of what a DOI concept FEMS 2006 Madrid, Spain Optimal data model provides semantic consistency Symposium 20. Biodiversity for true interoperability July 8, 2006
Ease of use No ongoing technical support Handle server must be installed and managed by local technical staff Free, but not without real costs The Digital Object Identifier System Turn-key application IDF and RAs maintain technical support staff Interacts with users, standards community and others Resolve problems of RAs and broader user community Underwrites cost of directory manager Support to RAs Guidance, troubleshooting, etc DOI Handbook Policies and procedures for various actors Guidelines for RAs, developers FEMS 2006 Madrid, Spain Developed by Symposium 20. Biodiversity federation of DOI agencies, July 8, 2006
Expressing relationships Provides support for multiple resolution Parent-child relationships Other relationships No preexisting constraints to make useful relationships The Digital Object Identifier System Provides framework to achieve practical application of multiple resolution Application of Handle System that adds the necessary constraints Constraints provided by metadata, which defines the entities (data dictionary approach) and expresses the relationships. FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Technical infrastructure The Digital Object Identifier System Provides a shared resolution service Global root servers, local Handle servers, clients, proxy servers Scalable and interoperable License provides a reference implementation but the database does Adds dedicated and improved technical not scale above a few million handles infrastructure Replication servers for RAs, secondary sites, mirror servers, proxy servers all housed in a secure commercial hosting facility More robust and scalable database DOI Directory Spain Manager to provide technical FEMS 2006 Madrid, Symposium 20. Biodiversity oversight 2006 evolutionary growth and July 8,
Semantic interoperability No requirements as to what is being identified No assurance of semantic interoperability across resources The Digital Object Identifier System Adds semantic interoperability across application space Feature of advanced DOI applications Provides metadata kernel to specify entity identified by DOI Optional tool to map existing schema through a structured ontology Ensures DOI can be the key in building multi component media objects or managing multiple assets Data dictionary and application framework Ensures that DOIs act predictably in applications with defined series IDF maintains indecs data dictionary and will likely maintain MPEG-21 data dictionary FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Development activities Provides upgrades of the global general-purpose naming system The Digital Object Identifier System Adds to this resource for active development of DOI applications and advanced features Working groups and technical support staff Use of DOIs in commercial settings RAs have an incentive to allocate their own resources to develop new features, collaborate with other RAs and share with the wider DOI community FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Costs to replicate a comparable system Need to add all preceding features not included in the general purpose software Cost of a production Handle license Other licenses to enabling technologies The Digital Object Identifier System Preceding features are part of a turn-key system RAs provide value added services to their clients IDF holds production Handle license with right to sublicense Cost of DOI assignment Vary across RAs and depend on their business model Can be free as part of a service offering FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Governance Independent of IDF Handle System Advisory Committee Major users and interested parties IDF is a member The Digital Object Identifier System Independent not-for-profit organization CNRI provides services under commercial agreement Elected board and nominated working groups Open membership Namesfor. Life, LLC is a general member FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Relevance of names in content Information retrieval Current web is designed for human-human communication Future web will rely on machines for information gathering, filtering, and knowledge discovery Need for semantic metadata for machine discovery and reasoning Keeping pace with the field Volume of content produced annually* Books - 8 Tbyte Journals - 2 Tbyte Semantic technologies N 4 L provides persistent semantic disambiguation Robust and economical There is a pressing need for automation *Scherf, et al. , (2005) Brief Bioinform. 6: 287 FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Find Organism Name in Code <p><b>VIRTUALLY all microorganisms. . . We report here the first structure determination, to our knowledge, of the siderophores from an open-ocean bacterium, alterobactin A and B from <em>Alteromonas luteoviolacea</em>. <em>A. luteoviolacea</em> is found in oligotrophic<sup>10</sup> and coastal<sup>11</sup> waters. Alterobactin A has an exceptionally high affinity constant for ferric ion. We suggest that at least some marine microorganisms may have developed higher-affinity iron chelators as part of an efficient iron uptake mechanism which is more effective than that of their terrestrial counterparts. </b> </p> FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Add N 4 L Tag Around Each Name to be Tracked <p><b>VIRTUALLY all microorganisms. . . We report here the first structure determination, to our knowledge, of the siderophores from an open-ocean bacterium, alterobactin A and B from <n 4 l: checkupdate doi=“ 10. 1601/nm. 2821”> <em>Alteromonas luteoviolacea</em></n 4 l: checkupdate>. <em>A. luteoviolacea</em> is found in oligotrophic<sup>10</sup> and coastal<sup>11</sup> waters. Alterobactin A has an exceptionally high affinity constant for ferric ion. We suggest that at least some marine microorganisms may have developed higher-affinity iron chelators as part of an efficient iron uptake mechanism which is more effective than that of their terrestrial counterparts. </b> </p> FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Comparing identifiers A single unambiguous string A label that identifies an entity A numbering scheme A method of providing consistent syntax to denote a class membership of an entity. ISBN 0 -387 -98771 -1 ATCC 27126 L-681, 572 A formal standard or industry convention ISBN numbers follow an international industry convention An arbitrary internal system Collection accession numbers and sample tracking numbers are typically institution specific Establishes a 1: 1 correspondence between labels and members Enumeration The number or label is simply a string FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Comparing identifiers (cont. ) An infrastructure specification A syntax by which an identifier can be expressed in a form suitable for use within a specific infrastructure. Actionable identifiers URI (URN and URL) ISBN numbers as UPC/EAN identifiers Does not mandate a method of creating labels Does not create a managed environment A fully implemented identifier system Includes Unique identifiers A formalized infrastructure Management policies for registration, structured interoperable metadata, policy, and governance mechanisms. Examples UPC/EAN barcodes and RFID tags Digital object identifiers (digital identifiers of objects) FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Globally unique identifiers (GUIDs) ARKs Archival resource keys Strengths - opaque, require metadata, identify an object Weakness - weak governance, not in widespread use, based on DNS, no guarantee of persistence, not standard a LSID Life science identifiers Strengths - opaque, identify an object, actionable Weakness - no governance, not in widespread use, based on DNS, no metadata requirement, no guarantee of persistence, not a standard PURL/POI Persistent URL/Persistent Object Identifier Strengths - opaque, identify an object, actionable, require metatdata Weakness - no governance, not in widespread use, based on DNS, no guarantee of persistence, not a standard FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Timeline for next phase of N 4 L development Q 1 1. 2 1. 3 1. 4 1. 5 1. 6 2. 1 2. 2 2. 3 2. 4 2. 5 3. 1 3. 2 3. 3 3. 4 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Database migration Automate name capture Ontology & schema development Incorporate partner data Deploy fault tolerant system Deploy to broader publications Determine FRS Change message system Client-side automated message processing Tag libraries PDF tools Upgrade web hub Partner content links Long-tail storefront New targets for N 4 L implementation FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Ramifications of misunderstanding a name or label Highly significant Wrong assumptions, assertions, or hypotheses Misdiagnosis of infectious diseases Misapplication of public policies Significant Lost opportunities Failure to reach potential customers potentially interested in marketed content, goods, and services at point of need. The long-tail phenomenon* Names trigger specific responses But, the concepts to which names apply are not static May not always map 1: 1 May require expertise for accurate interpretation FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Namesfor. Life The solution Leverages recent development in persistent identifier technology Unique mechanism Occurrence of a name triggers contextually appropriate retrieval services Uses embedded N 4 L-DOIs for content discovery Provides semantic enablement of existing content at minimal cost to data and content providers Through A unique combination of Identifiers Persistence Resolution FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Competing activities Technologies LSID - lack governance, persistence, limited usage Use covered in PCT/US 2005/001688 Can use N 4 L to resolve DOI <-> LSID Cross. Ref - bibliographic service, complementary to N 4 L TIB - DOIs on earth science data sets Not directly citable, only on supplementary data No semantic metadata (Dublin Core) Semantic web - bio-ontology initiatives NCBO, OBO, HCLS, GO, MGED Focus on gene and genome annotation Not designed for automated reasoning Initiatives TDWG/GBIF Focus on museums and herbaria Not supported by nomenclatural bodies Advocating use of LSID Attempting to duplicate the IDF/RA infrastructure to avoid cost of DOI FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Interactivity and navigation, heatmaps as a GUI FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Accessing the Namesfor. Life information objects FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Accessing the Namesfor. Life information objects FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
Accessing the Namesfor. Life information objects FEMS 2006 Madrid, Spain Symposium 20. Biodiversity July 8, 2006
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