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Community Support for Biodiversity Information
Management in South Africa
Willem Coetzer (SAIAB)
FBIP Forum, Pretoria, 3-4 June 2015
Captions: Arial, size 11, background
colour blue and font colour white
What are our objectives and what are the major discussion points?
Who uses Specify in South Africa? Who can use Specify and how can it be used?
Establishment of the Specify Support Group
Practical example of online, standardised biodiversity information:
Online Catalogue of Afrotropical Bees (A DwC Archive)
Demo of species information in Specify:
a) Taxon citations (for the GBIF ‘checklist dataset’, for taxonomic use)
b) Species information (for broader scientific, administrative, popular use)
Overview
What are our objectives?
• How is biodiversity information used (e.g. what products do we generate)?
• How can biodiversity information be standardised for better use / products?
• How must raw data be managed to generate these products?
What are the major (perceived) divisions?
• Physical specimens / observations
• Collection management / biodiversity informatics
• Specimens / species
• (Annotated) checklist (SA species); taxonomic revision. (A DwC dataset is
still unrefined)
• Darwin Core terms and DwC Archive. Biol. Coll. Ont. (developing)
• Mapping to the DwC terms is not sufficient. We need a good schema.
• Previously dwc:basisOfRecord; now dwc:occurrence -> dwc:hasEvidence
• Ditto, but at a higher level e.g. the community of atlassers
• We have successfully imported species info into Specify *
Community Support for Biodiversity Information
Management in South Africa
What are our objectives?
What are the major (perceived) divisions?
• (Annotated) checklist (SA species); taxonomic revision. (A DwC dataset is
not a product)
• Darwin Core terms and DwC Archive. Biol. Coll. Ont. (developing)
• Mapping to the DwC terms is not sufficient. We need a good schema.
Online Catalogue of Afrotropical Bees *
• Previously dwc:basisOfRecord; now dwc:occurrence -> dwc:hasEvidence
• Ditto, but at a higher level e.g. the community of atlassers
• We have successfully imported species info into Specify *
• Animals / plants• Specify makes no distinction, and offers excellent support for botanical data
Community Support for Biodiversity Information
Management in South Africa
Who uses Specify in South Africa? Who can use Specify and how can it be used?
Establishment of the Specify Support Group
What are our objectives?
What are the major (perceived) divisions?
• (Annotated) checklist (SA species); taxonomic revision. (A DwC dataset is
not a product)
• Darwin Core terms and DwC Archive. Biol. Coll. Ont. (developing)
• Mapping to the DwC terms is not sufficient. We need a good schema.
• Previously dwc:basisOfRecord; now dwc:occurrence -> dwc:hasEvidence
• Ditto, but at a higher level e.g. the community of atlassers
• We have successfully imported species info into Specify *
• Animals / plants
Online Catalogue of Afrotropical Bees *
Community Support for Biodiversity Information
Management in South Africa
Publishing standardized, enriched biodiversity
information
• A whole career of collecting and categorizing citations of bee
names
• textual Catalogue of Afrotropical Bees (Eardley and Urban
2010)
• The above model is outdated because increasingly machines,
rather than humans, exchange data with each other
• Hence the need for semantically enriched information (i.e.
consistent and rich meaning denoted by standardized terms)
• Biodiversity information MUST be standardized i.e. use
particular, accepted vocabularies of terms, mostly originating
from TDWG
• Darwin Core is the most significant and widely used, ratified
standard set of terms for sharing biodiversity data
Publishing standardized, enriched biodiversity
information
• Scientific names, citations, references, authors imported into
Specify 6 in 2010
• Data-cleansing and verification (2010-2013)
• Development of a system to transform these raw data in
Specify into enriched biodiversity information, specifically a
Darwin Core Archive which is displayed as a GBIF ‘checklist
dataset’
Catalogue of Afrtropical Bees
Taxon
(core)
Country
distribution
‘Description’
References
Type
specimens
or species
Structure of a Darwin Core Archive
Taxon
Distribution
Description
References
Types
ID 105763
acceptedNameUsageID
parentNameUsageID 102644
originalNameUsageID 105756
scientificName Hylaeus (Deranchylaeus) xanthostoma (Alfken)
acceptedNameUsage
parentNameUsage Hylaeus (Deranchylaeus) Bridwell, 1919
originalNameUsage Prosopis xanthostoma Alfken, 1914
namePublishedIn
Bridwell, J.C. 1919. Miscellaneous notes on
Hymenoptera with descriptions of new genera
and species. Proceedings of the Hawaiian
Entomological Society 4: 109-165
namePublishedInYear 1919
kingdom Animalia
phylum Arthropoda
class Insecta
order Hymenoptera
family Colletidae
genus Hylaeus
subgenus Deranchylaeus
specificEpithet xanthostoma
infraspecificEpithet
taxonRank species
scientificNameAuthorship (Alfken)
taxonomicStatus accepted
nomenclaturalStatus combinatio
Taxon
Core ID 105763
bibliographicCitation
Alfken, J.D. 1914. Zur Kenntnis der
afrikanischen Prosopis-Arten.
(Hym.). Deutsche Entomologische
Zeitschrift 2: 183-197
title
Zur Kenntnis der afrikanischen
Prosopis-Arten. (Hym.)
date 1914
subject Nomenclature
References
Core ID 105763
countryCode
BF, BI, BJ, BW, CD, CF, CM, ET, KE, MW,
NA, NG, SN, TZ, ZA, ZW
establishmentMeans native
source
Eardley, C.D. and R.P. Urban. 2010.
Catalogue of Afrotropical bees
(Hymenoptera: Apoidea: Apiformes).
Zootaxa 2455: 1-548
Distribution
Type specimens Description
Core ID 105763
type Ecology
description
Visits flowers of: Acacia nilotica, Acacia
tortilis, Aloe berhana, Borreria
verticillata, Harungana
madagascariensis, Pterolobium
stellatum, Veronica auriculifera,
Ziziphus mauritiana
Core ID 105763
bibliographicCitation
Friese, H. 1916. Chapter V:
Apidae. Beiträge zur Kenntnis der
Land-und Süsswasserfauna
Friederichsen & Co., Hamburg
title Chapter V: Apidae
date 1916
subject
Core ID 105763
bibliographicCitation
Bridwell, J.C. 1919. Miscellaneous
notes on Hymenoptera with
descriptions of new genera and
species. Proceedings of the
Hawaiian Entomological Society 4:
109-165
title
Miscellaneous notes on
Hymenoptera with descriptions of
new genera and species
date 1919
subject Nomenclature
Core ID 105763
bibliographicCitation
Cockerell, T.D.A. 1942. Bees of the
family Hylaeidae from the
Ethiopian Region. Smithsonian
Miscellaneous Collections 101: 1-
15
title
ZuBees of the family Hylaeidae
from the Ethiopian Regionr
Kenntnis der afrikanischen
Prosopis-Arten. (Hym.)
date 1942
subject
Core ID 105763
bibliographicCitation
Snelling, R.R. 1985. The
systematics of the hylaeine bees
(Hymenoptera: Colletidae) of the
Ethiopian zoogeographical region:
The genera and subgenera with
revisions of the smaller groups.
Contributions in Science, Natural
History Museum of Los Angeles
County 361: 1-33
title
The systematics of the hylaeine
bees (Hymenoptera: Colletidae) of
the Ethiopian zoogeographical
region: The genera and subgenera
with revisions of the smaller
groups
date 1985
subject
Core ID 105763
bibliographicCitation
Eardley, C.D. and R.P. Urban.
2010. Catalogue of Afrotropical
bees (Hymenoptera: Apoidea:
Apiformes). Zootaxa 2455: 1-548
title
Catalogue of Afrotropical bees
(Hymenoptera: Apoidea:
Apiformes)
date 2010
subject
Core ID 105763
bibliographicCitation
Alfken, J.D. 1914. Zur Kenntnis der
afrikanischen Prosopis-Arten.
(Hym.). Deutsche Entomologische
Zeitschrift 2: 183-197
title
Zur Kenntnis der afrikanischen
Prosopis-Arten. (Hym.)
date 1914
subject Nomenclature
Core ID 105763
bibliographicCitation
Medler, J.T. 1980. Insects of
Nigeria—Checklist and
bibliography. Memoirs of the
American Entomological Institute
30: 1-919
title
Insects of Nigeria—Checklist and
bibliography
date 1980
subject
Taxon
Distribution
Description
References
Types
Taxon
ID 105756
acceptedNameUsageID 105763
parentNameUsageID 113143
originalNameUsageID
scientificName Prosopis xanthostoma Alfken, 1914
acceptedNameUsage Hylaeus (Deranchylaeus) xanthostoma (Alfken)
parentNameUsage Prosopis Fabricius, 1804
originalNameUsage
namePublishedIn
Alfken, J.D. 1914. Zur Kenntnis der
Afrikanischen Prosopis-Arten. (Hym.). Deutsche
Entomologische Zeitschrift 2: 183-197
namePublishedInYear 1914
kingdom Animalia
phylum Arthropoda
class Insecta
order Hymenoptera
family Colletidae
genus Prosopis
subgenus
specificEpithet xanthostoma
infraspecificEpithet
taxonRank species
scientificNameAuthorship Alfken, 1914
taxonomicStatus Homotypic synonym
nomenclaturalStatus valid
Core ID 105756
bibliographicCitation
Alfken, J.D. 1914. Zur Kenntnis der
Afrikanischen Prosopis-Arten.
(Hym.). Deutsche Entomologische
Zeitschrift 2: 183-197
title
Zur Kenntnis der Afrikanischen
Prosopis-Arten. (Hym.)
date 1914
subject Nomenclature
References Distribution
Type specimens Description
Core ID 105756
typestatus lectotype
typeDesignationType
typeDesignatedBy
Dathe, H.H. 2014. Studies on the
systematics and taxonomy of the
genus Hylaeus F. (8) Revision of
the Afrotropic subgenus Hylaeus
(Deranchylaeus) Bridwell
(Hymenoptera: Anthophila,
Colletidae). Zootaxa 3874: 1-84
scientificName Prosopis xanthostoma
taxonRank species
bibliographicCitation
collectionCode MNHU
locality Democratic Republic of the Congo
sex female
Accepted NameSynonym

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Fbip specify2015

  • 1. Community Support for Biodiversity Information Management in South Africa Willem Coetzer (SAIAB) FBIP Forum, Pretoria, 3-4 June 2015 Captions: Arial, size 11, background colour blue and font colour white
  • 2. What are our objectives and what are the major discussion points? Who uses Specify in South Africa? Who can use Specify and how can it be used? Establishment of the Specify Support Group Practical example of online, standardised biodiversity information: Online Catalogue of Afrotropical Bees (A DwC Archive) Demo of species information in Specify: a) Taxon citations (for the GBIF ‘checklist dataset’, for taxonomic use) b) Species information (for broader scientific, administrative, popular use) Overview
  • 3. What are our objectives? • How is biodiversity information used (e.g. what products do we generate)? • How can biodiversity information be standardised for better use / products? • How must raw data be managed to generate these products? What are the major (perceived) divisions? • Physical specimens / observations • Collection management / biodiversity informatics • Specimens / species • (Annotated) checklist (SA species); taxonomic revision. (A DwC dataset is still unrefined) • Darwin Core terms and DwC Archive. Biol. Coll. Ont. (developing) • Mapping to the DwC terms is not sufficient. We need a good schema. • Previously dwc:basisOfRecord; now dwc:occurrence -> dwc:hasEvidence • Ditto, but at a higher level e.g. the community of atlassers • We have successfully imported species info into Specify * Community Support for Biodiversity Information Management in South Africa
  • 4. What are our objectives? What are the major (perceived) divisions? • (Annotated) checklist (SA species); taxonomic revision. (A DwC dataset is not a product) • Darwin Core terms and DwC Archive. Biol. Coll. Ont. (developing) • Mapping to the DwC terms is not sufficient. We need a good schema. Online Catalogue of Afrotropical Bees * • Previously dwc:basisOfRecord; now dwc:occurrence -> dwc:hasEvidence • Ditto, but at a higher level e.g. the community of atlassers • We have successfully imported species info into Specify * • Animals / plants• Specify makes no distinction, and offers excellent support for botanical data Community Support for Biodiversity Information Management in South Africa
  • 5. Who uses Specify in South Africa? Who can use Specify and how can it be used? Establishment of the Specify Support Group What are our objectives? What are the major (perceived) divisions? • (Annotated) checklist (SA species); taxonomic revision. (A DwC dataset is not a product) • Darwin Core terms and DwC Archive. Biol. Coll. Ont. (developing) • Mapping to the DwC terms is not sufficient. We need a good schema. • Previously dwc:basisOfRecord; now dwc:occurrence -> dwc:hasEvidence • Ditto, but at a higher level e.g. the community of atlassers • We have successfully imported species info into Specify * • Animals / plants Online Catalogue of Afrotropical Bees * Community Support for Biodiversity Information Management in South Africa
  • 6. Publishing standardized, enriched biodiversity information • A whole career of collecting and categorizing citations of bee names • textual Catalogue of Afrotropical Bees (Eardley and Urban 2010) • The above model is outdated because increasingly machines, rather than humans, exchange data with each other • Hence the need for semantically enriched information (i.e. consistent and rich meaning denoted by standardized terms)
  • 7. • Biodiversity information MUST be standardized i.e. use particular, accepted vocabularies of terms, mostly originating from TDWG • Darwin Core is the most significant and widely used, ratified standard set of terms for sharing biodiversity data Publishing standardized, enriched biodiversity information
  • 8. • Scientific names, citations, references, authors imported into Specify 6 in 2010 • Data-cleansing and verification (2010-2013) • Development of a system to transform these raw data in Specify into enriched biodiversity information, specifically a Darwin Core Archive which is displayed as a GBIF ‘checklist dataset’ Catalogue of Afrtropical Bees
  • 10. Taxon Distribution Description References Types ID 105763 acceptedNameUsageID parentNameUsageID 102644 originalNameUsageID 105756 scientificName Hylaeus (Deranchylaeus) xanthostoma (Alfken) acceptedNameUsage parentNameUsage Hylaeus (Deranchylaeus) Bridwell, 1919 originalNameUsage Prosopis xanthostoma Alfken, 1914 namePublishedIn Bridwell, J.C. 1919. Miscellaneous notes on Hymenoptera with descriptions of new genera and species. Proceedings of the Hawaiian Entomological Society 4: 109-165 namePublishedInYear 1919 kingdom Animalia phylum Arthropoda class Insecta order Hymenoptera family Colletidae genus Hylaeus subgenus Deranchylaeus specificEpithet xanthostoma infraspecificEpithet taxonRank species scientificNameAuthorship (Alfken) taxonomicStatus accepted nomenclaturalStatus combinatio Taxon Core ID 105763 bibliographicCitation Alfken, J.D. 1914. Zur Kenntnis der afrikanischen Prosopis-Arten. (Hym.). Deutsche Entomologische Zeitschrift 2: 183-197 title Zur Kenntnis der afrikanischen Prosopis-Arten. (Hym.) date 1914 subject Nomenclature References Core ID 105763 countryCode BF, BI, BJ, BW, CD, CF, CM, ET, KE, MW, NA, NG, SN, TZ, ZA, ZW establishmentMeans native source Eardley, C.D. and R.P. Urban. 2010. Catalogue of Afrotropical bees (Hymenoptera: Apoidea: Apiformes). Zootaxa 2455: 1-548 Distribution Type specimens Description Core ID 105763 type Ecology description Visits flowers of: Acacia nilotica, Acacia tortilis, Aloe berhana, Borreria verticillata, Harungana madagascariensis, Pterolobium stellatum, Veronica auriculifera, Ziziphus mauritiana Core ID 105763 bibliographicCitation Friese, H. 1916. Chapter V: Apidae. Beiträge zur Kenntnis der Land-und Süsswasserfauna Friederichsen & Co., Hamburg title Chapter V: Apidae date 1916 subject Core ID 105763 bibliographicCitation Bridwell, J.C. 1919. Miscellaneous notes on Hymenoptera with descriptions of new genera and species. Proceedings of the Hawaiian Entomological Society 4: 109-165 title Miscellaneous notes on Hymenoptera with descriptions of new genera and species date 1919 subject Nomenclature Core ID 105763 bibliographicCitation Cockerell, T.D.A. 1942. Bees of the family Hylaeidae from the Ethiopian Region. Smithsonian Miscellaneous Collections 101: 1- 15 title ZuBees of the family Hylaeidae from the Ethiopian Regionr Kenntnis der afrikanischen Prosopis-Arten. (Hym.) date 1942 subject Core ID 105763 bibliographicCitation Snelling, R.R. 1985. The systematics of the hylaeine bees (Hymenoptera: Colletidae) of the Ethiopian zoogeographical region: The genera and subgenera with revisions of the smaller groups. Contributions in Science, Natural History Museum of Los Angeles County 361: 1-33 title The systematics of the hylaeine bees (Hymenoptera: Colletidae) of the Ethiopian zoogeographical region: The genera and subgenera with revisions of the smaller groups date 1985 subject Core ID 105763 bibliographicCitation Eardley, C.D. and R.P. Urban. 2010. Catalogue of Afrotropical bees (Hymenoptera: Apoidea: Apiformes). Zootaxa 2455: 1-548 title Catalogue of Afrotropical bees (Hymenoptera: Apoidea: Apiformes) date 2010 subject Core ID 105763 bibliographicCitation Alfken, J.D. 1914. Zur Kenntnis der afrikanischen Prosopis-Arten. (Hym.). Deutsche Entomologische Zeitschrift 2: 183-197 title Zur Kenntnis der afrikanischen Prosopis-Arten. (Hym.) date 1914 subject Nomenclature Core ID 105763 bibliographicCitation Medler, J.T. 1980. Insects of Nigeria—Checklist and bibliography. Memoirs of the American Entomological Institute 30: 1-919 title Insects of Nigeria—Checklist and bibliography date 1980 subject
  • 11. Taxon Distribution Description References Types Taxon ID 105756 acceptedNameUsageID 105763 parentNameUsageID 113143 originalNameUsageID scientificName Prosopis xanthostoma Alfken, 1914 acceptedNameUsage Hylaeus (Deranchylaeus) xanthostoma (Alfken) parentNameUsage Prosopis Fabricius, 1804 originalNameUsage namePublishedIn Alfken, J.D. 1914. Zur Kenntnis der Afrikanischen Prosopis-Arten. (Hym.). Deutsche Entomologische Zeitschrift 2: 183-197 namePublishedInYear 1914 kingdom Animalia phylum Arthropoda class Insecta order Hymenoptera family Colletidae genus Prosopis subgenus specificEpithet xanthostoma infraspecificEpithet taxonRank species scientificNameAuthorship Alfken, 1914 taxonomicStatus Homotypic synonym nomenclaturalStatus valid Core ID 105756 bibliographicCitation Alfken, J.D. 1914. Zur Kenntnis der Afrikanischen Prosopis-Arten. (Hym.). Deutsche Entomologische Zeitschrift 2: 183-197 title Zur Kenntnis der Afrikanischen Prosopis-Arten. (Hym.) date 1914 subject Nomenclature References Distribution Type specimens Description Core ID 105756 typestatus lectotype typeDesignationType typeDesignatedBy Dathe, H.H. 2014. Studies on the systematics and taxonomy of the genus Hylaeus F. (8) Revision of the Afrotropic subgenus Hylaeus (Deranchylaeus) Bridwell (Hymenoptera: Anthophila, Colletidae). Zootaxa 3874: 1-84 scientificName Prosopis xanthostoma taxonRank species bibliographicCitation collectionCode MNHU locality Democratic Republic of the Congo sex female