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Monitoring and MeasuringBiodiversity: Some Thoughts        Donat Agosti  Beheshty University, Tehran      February 21, 2011
Do you know ...
Earth Summit
IPBES
NCBI
GBIF
TDWG
Darwin Core
They all have to do withglobal biodiversity issues
Earth SummitRio Earth Summit 1992:Global Biodiversity CrisisConvention on Biological Diversity
IPBESIntergovernmental Platform on  Biodiversity and Ecoystem  ServicesTool to assess global biodiversity  patterns and ch...
NCBINational Center for Biotechnology InformationGlobal resource for molecular biology information (eg GenBank)
GBIFGlobal Biodiversity Information FacilityAccess point to specimen data
http://data.gbif.org/countries/IR
TDWGTaxonomic Data Working GroupBody to create standards to exchange data to build highly distributed global information s...
Darwin CoreGlobal standard to describe specimen data needed for exchange
An example from the Neurocommons text miningpilot:• PubMed abstracts: > 16,000,000• CNS classified abstracts: 874,727• tex...
“protein-proteininteraction networks”          John Wilbanks,          Neurocommons
This is the world we live in:A truly global community where machines can do an unimaginable amount of work.
It has its dangers:We are not all the same
It has its dangers:We are not all the sameIt has its advantages:All events can be put in context.
Is something a local, regional or  global event?
Is something a local, regional or  global event?Connecting time series (local) with  spatial data
Is something a local, regional or  global event?Or is it just a fluctuation or  artifact?
Monitoring as a comparative science
Monitoring as a comparative scienceChange over timeChange over land use
What kind of and                                       how many ants?          Δt ?                              Δt ?     ...
What does it mean?ScienceStandard sampling
Standard repetitive samples
What does it mean?ScienceStandard samplingQuality control
What does it mean?ScienceStandard samplingQuality controlStandards for data descriptionExchange protocols
What does it mean?ScienceStandard samplingQuality controlStandards for data description
http://www.sciencemag.org/content/331/6018/703.full.html
selamatbonjour                ciao  salam             helo
What does it mean?ScienceStandard samplingQuality controlStandards for data descriptionExchange protocols
Plazi Search and Retrieval   Server: Access to data                        TAPIR, SPM                                     ...
What do we need?Access
Before antbase.org, Harvard„s Museum ofComparative Zoology could claim to be the onlylocation with a complete set of ant s...
What do we need for monitoring?Access Identification aids
Who are you?                            What do you do?              Who is this? Where are you                           ...
What do we need for monitoring?Access Identification aids   What species is it?
Semantic, enhanced treatments do            the job ...
What do we need monitoring?Access Identification aids   What species is it? What do I know about the species?
What do we need for monitoring?Access Identification aids   What species is it? What do I know about the species? Where do...
What do we need for monitoring?AccessMetadata
What do we need for monitoring?AccessMetadata Describing the data; also to discover it
Linnaeus, C., 1758, Systema naturae. Regnum Animale. 10 th ed., W. Engelmann, Lipsiae,<tax:taxonx xsi:schemaLocation="http...
What do we need monitoring?AccessMetadataNetworks get info – provide info
What do we need for monitoring?AccessMetadataNetworks get info – provide info use standards
What kind of ants live in Iran?
Standards                        „Iran ants“:Use iran ants in google 495,000 recordsShow iran ants in plazi.org
Semantic, XML enhancedtreatments do the job ...
This can also be applied to entire sections of text, such as  the treatment of a species and its parts.                   ...
What do we need for monitoring?Networks get info – provide info use standards use open access / open source
What do we need monitoring?Social networks Information is not free in the sense of „it doesn‘t cost anything“
What do we need?Social networks  Information is not free in the  sense of „it doesn‘t cost anything“ Information depends o...
Monitoring biodiversity depends foremost on science...
Monitoring biodiversity depends foremost on science (and good scientists)...... technology makes it just more  relevant an...
Biodiversity data at work:The use of our monitoring data by IPBES is an indication that we deliver data and information th...
With my best thanks!    Donat Agosti agosti@amnh.org  http://plazi.org http://antbase.org
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
20110222 behesty monitoring and measuring biodiversity
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20110222 behesty monitoring and measuring biodiversity

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lecture presented at Shahid Beheshti University, Tehran, Iran. Feb 22, 2011

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20110222 behesty monitoring and measuring biodiversity

  1. 1. Monitoring and MeasuringBiodiversity: Some Thoughts Donat Agosti Beheshty University, Tehran February 21, 2011
  2. 2. Do you know ...
  3. 3. Earth Summit
  4. 4. IPBES
  5. 5. NCBI
  6. 6. GBIF
  7. 7. TDWG
  8. 8. Darwin Core
  9. 9. They all have to do withglobal biodiversity issues
  10. 10. Earth SummitRio Earth Summit 1992:Global Biodiversity CrisisConvention on Biological Diversity
  11. 11. IPBESIntergovernmental Platform on Biodiversity and Ecoystem ServicesTool to assess global biodiversity patterns and change
  12. 12. NCBINational Center for Biotechnology InformationGlobal resource for molecular biology information (eg GenBank)
  13. 13. GBIFGlobal Biodiversity Information FacilityAccess point to specimen data
  14. 14. http://data.gbif.org/countries/IR
  15. 15. TDWGTaxonomic Data Working GroupBody to create standards to exchange data to build highly distributed global information systems
  16. 16. Darwin CoreGlobal standard to describe specimen data needed for exchange
  17. 17. An example from the Neurocommons text miningpilot:• PubMed abstracts: > 16,000,000• CNS classified abstracts: 874,727• text mining recognized: 368,688• text mining processed: 94,381• extracted graph of 30,000+ relationships and 5,500genes and proteins “protein-protein interaction networks” John Wilbanks, Neurocommons
  18. 18. “protein-proteininteraction networks” John Wilbanks, Neurocommons
  19. 19. This is the world we live in:A truly global community where machines can do an unimaginable amount of work.
  20. 20. It has its dangers:We are not all the same
  21. 21. It has its dangers:We are not all the sameIt has its advantages:All events can be put in context.
  22. 22. Is something a local, regional or global event?
  23. 23. Is something a local, regional or global event?Connecting time series (local) with spatial data
  24. 24. Is something a local, regional or global event?Or is it just a fluctuation or artifact?
  25. 25. Monitoring as a comparative science
  26. 26. Monitoring as a comparative scienceChange over timeChange over land use
  27. 27. What kind of and how many ants? Δt ? Δt ? What is the impact ofΔt ? land use change? Δ? Δt ? What happens over time? Δt ? What happens overForest Urban areas space and time?Pasture CampusCacao / Cabruca
  28. 28. What does it mean?ScienceStandard sampling
  29. 29. Standard repetitive samples
  30. 30. What does it mean?ScienceStandard samplingQuality control
  31. 31. What does it mean?ScienceStandard samplingQuality controlStandards for data descriptionExchange protocols
  32. 32. What does it mean?ScienceStandard samplingQuality controlStandards for data description
  33. 33. http://www.sciencemag.org/content/331/6018/703.full.html
  34. 34. selamatbonjour ciao salam helo
  35. 35. What does it mean?ScienceStandard samplingQuality controlStandards for data descriptionExchange protocols
  36. 36. Plazi Search and Retrieval Server: Access to data TAPIR, SPM You You human machine You
  37. 37. What do we need?Access
  38. 38. Before antbase.org, Harvard„s Museum ofComparative Zoology could claim to be the onlylocation with a complete set of ant systematicspublications from 1758 - present.Through antbase.org„sdigital library, accessto this body ofliterature is worldwide,and it is actively used(>10,000 visits in onemonth only).
  39. 39. What do we need for monitoring?Access Identification aids
  40. 40. Who are you? What do you do? Who is this? Where are you from? What do I know about her? Where does she live?
  41. 41. What do we need for monitoring?Access Identification aids What species is it?
  42. 42. Semantic, enhanced treatments do the job ...
  43. 43. What do we need monitoring?Access Identification aids What species is it? What do I know about the species?
  44. 44. What do we need for monitoring?Access Identification aids What species is it? What do I know about the species? Where does it live?
  45. 45. What do we need for monitoring?AccessMetadata
  46. 46. What do we need for monitoring?AccessMetadata Describing the data; also to discover it
  47. 47. Linnaeus, C., 1758, Systema naturae. Regnum Animale. 10 th ed., W. Engelmann, Lipsiae,<tax:taxonx xsi:schemaLocation="http://www.taxonx.org/schema/v1 http://www.taxonx.org/schema/v1/taxonx1.xsd http://www.loc.gov/mods/v3 http://www.loc.gov/mods/v3/mods-3-1.xsd http://digir.net/schema/conceptual/darwin/2003/1.0 http://digir.net/schema/conceptual/darwin/2003/1.0/darwin2.xsd"><tax:taxonxHeader> <mods:mods> <mods:titleInfo> <mods:title>Systema naturae. Regnum Animale. 10 th ed.</mods:title> </mods:titleInfo> <mods:name type="personal"> <mods:role> <mods:roleTerm>Author</mods:roleTerm> </mods:role> <mods:namePart>Linnaeus, C.</mods:namePart> </mods:name> <mods:originInfo> <mods:dateIssued>1758</mods:dateIssued> <mods:publisher>W. Engelmann</mods:publisher> <mods:place> <mods:placeTerm type="text">Lipsiae</mods:placeTerm> </mods:place>
  48. 48. What do we need monitoring?AccessMetadataNetworks get info – provide info
  49. 49. What do we need for monitoring?AccessMetadataNetworks get info – provide info use standards
  50. 50. What kind of ants live in Iran?
  51. 51. Standards „Iran ants“:Use iran ants in google 495,000 recordsShow iran ants in plazi.org
  52. 52. Semantic, XML enhancedtreatments do the job ...
  53. 53. This can also be applied to entire sections of text, such as the treatment of a species and its parts. <tax:treatment> <tax:nomenclature> <tax:name> <tax:xid source="HNS" identifier="19 <tax:xmldata> <dc:Genus>Mystrium</dc:Genus> <dc:Species>leonie</dc:Species> </tax:xmldata> Mystrium leonie </tax:name> <tax:status>n. sp.</tax:status> Fig 1 D - F </tax:nomenclature> <tax:div type="description"> <tax:p>HOLOTYPE WORKER: TL 3.95, H 1.30, SI 137, PW 0.73, ML 0.38. Mand
  54. 54. What do we need for monitoring?Networks get info – provide info use standards use open access / open source
  55. 55. What do we need monitoring?Social networks Information is not free in the sense of „it doesn‘t cost anything“
  56. 56. What do we need?Social networks Information is not free in the sense of „it doesn‘t cost anything“ Information depends on you!
  57. 57. Monitoring biodiversity depends foremost on science...
  58. 58. Monitoring biodiversity depends foremost on science (and good scientists)...... technology makes it just more relevant and powerful.
  59. 59. Biodiversity data at work:The use of our monitoring data by IPBES is an indication that we deliver data and information that can be used beyond our own work to save planet earth.
  60. 60. With my best thanks! Donat Agosti agosti@amnh.org http://plazi.org http://antbase.org

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