Occurrence datasets/ datasources published through DWB BioCASe Data Publication pipeline#

The DWB BioCASe Data Publication pipeline and RDF service are introduced here. A more detailed description of the content of each single dataset is given in the tables below.

The services at the SNSB IT Center are based on an SNSB installation of the BioCASE Provider Software (BPS). It has a simple user interface Local Query Tool to query the local pywrapped databases (=data resources; DWB PostgreSQL cache databases). 48 datasources or datasets are currently integrated. Each of these represents a database "project" mapped to the conceptual schema ABCD. The mapping is done based on the Identification Unit as core Unit not on the Specimen Unit with the ABCD element "Unit GUID" as stable identifier. The original data are managed in a number of MS DWB production databases on several instances, installed on MS VMs (e.g., BFL, SNSB+extern, SMNS, SMNK, TNT, ZSM).

With that pipeline more than 6,5 million data records with UnitIDs are accessible through the GBIF portal. The BioCASe Downloads Counter for GBIF lists the downloads of data from GBIF data publishers with BioCASe software installation. Various sets of these data are accessible through additional data access points with the technical power to deliver the BioCAse proceessed data, especially when these are based on the ABCD standard. One example is The Biological Collection Access Service for Europe, providing access to European biodiversity data. Some of the datasets listed in the tables below are also offered via GFBio data pipelines *****.


 

Please contact Tanja Weibulat for general support concerning the use of DWB and the data flow concerned; Dieter Neubacher (system administrator), Dr. Stefan Seifert (system administrator) and Dr. Markus Weiss (Diversity Workbench databases administrator) are responsible for the technical concept and administration of the DWB BioCASe Data Publication Services.

 


 

SNSB Owned BSM Datasources#

Datasource Description Data Curators BPS Local Query Tool (+/- UnitGUID of SNSB id service) Datasource Access in GBIF GBIF DOI Datasource Access in GFBio DC Master (Internal Access): IdentifUnits/UnitParts (GeorefUnits) {date} Specific Features
BSMeryscoll - About D. Triebel BSMeryscoll - BPS (+) GBIF doi:10.15468/sookye GFBio 11.844 (10.691) unit based {2018-09-10} 2 IdentifUnits, LIASnames, exsiccatae
BSMfungicoll - About D. T. BSMfungicoll - BPS (+) GBIF doi:10.15468/zinzhd GFBio 23.359 (19.069) unit based {2018-09-10} 2 IdentifUnits, exsiccatae, type status
BSMgrossebrcoll - About D. T. BSMgrossebr - BPS (+) GBIF doi:10.15468/onfqgb - 10.851 (10.677) unit based {2018-09-10} locality field of half of the data records still empty, all records georeferenced by using DiversityGazetteers
BSMlichenscoll - About A. Beck BSMlichenscoll - BPS (+) GBIF doi:10.15468/lqetda GFBio 23.135 (10.904) unit based {2018-09-10} LIASnames, exsiccatae, type status
BSMlichfungicoll - About D. T. BSMlichfungicoll - BPS (+) GBIF doi:10.15468/ni5yho - 9.352 (8.458) unit based {2018-09-10} 2-3(-x) IdentifUnits, LIASnames, exsiccatae, type status
BSMmicrofexscoll - About D. T. BSMmicrofexscoll - BPS (+) GBIF doi:10.15468/qxmief - 2.066 (2.056) unit based {2018-09-10} 2-3(-x) IdentifUnits, LIASnames, exsiccatae
BSMmyxmaincoll - About D. T. BSMmyxmaincoll - BPS (+) GBIF doi:10.15468/zdcclb GFBio 6.824 (5.514) part based {2018-09-10} exsiccatae
BSMneubert - About D. T. BSMneubert - BPS (+) GBIF doi:10.15468/sh9r0c - 12.728 (12.385) part based {2018-09-10} +- without images
BSMschiefcoll - About D. T. BSMschiefcoll - BPS (+) GBIF doi:10.15468/342g8j - 1.910 (1.909) unit based {2018-09-10} water colours
BSMschnittler - About M. Schnittler, D. T. BSMschnittler - BPS (+) GBIF doi:10.15468/xquobe - 5.255 (5.002) unit based {2018-09-10} +- without images
BSMvplantscoll - About H.-J. Esser, Fleischmann, A. & Schuhwerk, F. (†) BSMvplantscoll - BPS (+) GBIF doi:10.15468/vgr4kl GFBio 72.062 (54.614) unit based {2018-09-10} type status, images of herbarium sheets
BSMweinzierlcoll - About D. T. BSMweinzierlcoll - BPS (+) GBIF doi:10.15468/dixlft - 13.323 (12.504) part based {2018-09-10} diatoms, images of slides, LM images
BSMwohlfcoll - About D. T. BSMwohlfcoll - BPS (+) GBIF doi:10.15468/vldzvk - 1.910 (1.810) part based {2018-09-10} water colours

SNSB Owned BSM Datasources - DiversityIndexing#

Datasource Description Data Curators BPS Local Query Tool (+/- UnitGUID of SNSB id service) Datasource Access in GBIF GBIF DOI Datasource Access in GFBio DC Master (Internal Access): IdentifUnits/UnitParts (GeorefUnits) {date} Specific Features
GBIFdoppelbaur - About G. Hagedorn, D. T. DiversityIndexing_GBIFdoppelbaur - BPS (-) GBIF doi:10.15468/0ui67r - 21.348 {2018-09-09} observations

 

SNSB Owned Datasources (excl. BSM) #

Datasource Description Data Curators BPS Local Query Tool (+/- UnitGUID of SNSB id service) Datasource Access in GBIF GBIF DOI Datasource Access in GFBio DC Master (Internal Access): IdentifUnits/UnitParts (GeorefUnits) {date} Specific Features
BSPGcoll - About A. Nützel BSPGcoll - BPS (+) GBIF doi:10.15468/mw2ak8 - 8.225 (696) unit based {2018-09-10} +- without images, type status, stratigraphy, fossils
BSPGpiscescoll - About M. Moser BSPGpiscescoll - BPS (+) GBIF doi:10.15468/wskrvt GFBio 2.463 (2.278) part based {2018-09-10} with images, stratigraphy, fossils
JMEpiscescoll - About M. Kölbl-Ebert JMEpiscescoll - BPS (+) GBIF doi:10.15468/qi5so7 GFBio 7.591 (7.147) part based {2018-09-10} with images, stratigraphy, fossils
SAPMmammaliacoll - About H. Obermaier SAPMmammaliacoll - BPS (+) GBIF doi:10.15468/elc2yx GFBio 3.192 (79) part based {2018-09-10} +- without images
SAPMpiscescoll - About H. Obermaier SAPMpiscescoll - BPS (+) GBIF doi:10.15468/uxag7k GFBio 4.162 (2.750) part based {2018-09-10} with images
ZSMarthrovariacoll - About R. Melzer, J. Spelda ZSMarthrovariacoll - BPS (+) GBIF doi:10.15468/hrzzrc GFBio 21.262 (8.328) part based {2018-09-10} with high resolution macro images and LM images
ZSMavstudiescoll - About J. Spelda ZSMavstudiescoll - BPS (+) GBIF doi:10.15468/biecak - 26.534 (26.534) part based {2018-09-10} environmental samples
ZSMbfbcoll - About J. Morinière, J. Spelda ZSMbfbcoll - BPS (+) no GBIF access intended, but data provision for GFBio - GFBio 13.603 (13.174) part based {2018-09-10} DNA samples, BOLD Download 2015; see also http://www.gbif.org/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661 (from 2013)
ZSMpiscescoll - About D. Neumann ZSMpiscescoll - BPS (+) GBIF doi:10.15468/fzn9sv GFBio 72.994 (58.356) part based {2018-09-10} -

SNSB Hosted Datasources#

Datasource Description Data Curators BPS Local Query Tool (+/- UnitGUID of SNSB id service) Datasource Access in GBIF GBIF DOI Datasource Access in GFBio DC Master (Internal Access): IdentifUnits/UnitParts (GeorefUnits) {date} Specific Features
BFLportal01coll - About W. Ahlmer, M. Ruff BFLportal01coll - BPS (+) GBIF doi:10.15468/osi63h GFBio 5.518.839 (5.509.329) unit based {2018-09-10} monitoring data "Flora of Bavaria", verunschärft; 2.667 Images
BFLportal04coll - About Bayerisches Landesamt für Umwelt BFLportal04coll - BPS (+) *** *** GFBio *** (***) unit based {2018-09-26} monitoring data "Flora of Bavaria", verunschärft
BIOTAlichencoll - About A. Beck, L. Zedda BIOTAlichencoll - BPS (+) GBIF doi:10.15468/kosycz - 2.246 (2.218) unit based {2018-09-10} 1-2 IdentifUnits per specimen, LIASnames, more than 1 image per IdentifUnit
Blettaucoll - About H. Sipman Blettaucoll - BPS (+) GBIF doi:10.15468/ed17cn - 9.654 (9.651) unit based {2018-09-10} 2-more IdentifUnits per specimen, LIASnames
GOETbryocoll - About --- to be delivered soon ?? M. Appelhans & E. Reiner-Drehwald GOETbryocoll - BPS (-) GBIF doi:? - 1.248 (0) unit based {2018-09-10} bryophytes specimens, type status, high resolution images of herbarium sheets; new dynamic data provision for GBIF (former version available under http://www.gbif.org/publisher/59c81290-df0e-11d8-b22e-b8a03c50a862; this version is outdated?)
GOETvplantscoll - About M. Appelhans GOETvplantscoll - BPS (-) GBIF doi:10.15468/9uzqe3 GFBio 25.295 (2.015) unit based {2018-09-10} vascular plants specimens, type status, high resolution images of herbarium sheets; new dynamic data provision for GBIF (former version available under http://www.gbif.org/publisher/59c81290-df0e-11d8-b22e-b8a03c50a862; this version is outdated?)
GLMcoll - About H. Boyle GLMcoll - BPS (+) GBIF doi:10.15468/fhmwzv - 165.155 (142.983) unit based {2018-09-10} +- without images, subgeneric units
HALcoll - About U. Braun HALcoll - BPS (+) GBIF doi:10.15468/gccftu - 2.940 (2.912) unit based {2018-09-10} 2 IdentifUnits, +- without images, LIASnames
HYMIScoll - About --- to be delivered soon S. Schmidt HYMIScoll - BPS (+) GBIF doi:?- 3.520 (13) unit based {2018-09-10} -
JMRCfungicoll About K. Voigt JMRCfungicoll - BPS (+) GBIF doi:10.15468/dmxfwk - 28.159 (0) part based {2018-09-10} culture collection
LEmyxcoll - About Y. Novozhilov LEmyxcoll - BPS (+) GBIF doi:10.15468/i83r9k - 16.698 (16.519) unit based {2018-09-10} +- without images
MBcoll - About K. Rexer MBcoll - BPS (+) GBIF doi:10.15468/lxnnnf GFBio 50.306 (16.087) unit based {2018-09-10} +- without images, often 2 units, but only one preserved and delivered for GBIF
Morphyllcoll - About C. Traiser Morphyllcoll - BPS (-) - - 1.853 (1.852) part based {2018-09-10} -
MSBvplantscoll - About H.-J. Esser, A. Fleischmann, F. Schuhwerk (†) MSBvplantscoll - BPS (+) GBIF doi:10.15468/trfgn8 GFBio 1.815 (41) unit based {2018-09-10} type status, images of herbarium sheets
REGvplantscoll - About H. Gigglberger (†) REGvplantscoll - BPS (+) GBIF doi:10.15468/rv6kzy - 3.119 (0) unit based {2018-09-10} type status, images of herbarium sheets; 13.3.15: 1000 types from Africa with images added (not high resolution) (originally mobilised for GPI)
SMNKfungicoll - About (neu) SMNKfungicoll - About (alt) M. Scholler SMNKfungicoll - BPS (-) GBIF doi:10.15468/0bhhip - 72.178 (67.412) unit based {2018-09-10} 2 IdentifUnits
SMNKspidercoll - About H. Höfer SMNKspidercoll - BPS (-) GBIF doi:10.15468/fmxx2i GFBio 19.680 (17.645) unit based {2018-09-10} with images
SMNKspiderstudcoll - About H. Höfer SMNKspiderstudcoll - BPS (-) GBIF doi:10.15468/pr26sz GFBio 55.877 (55.643) unit based {2018-09-10} -
SMNS-E-araneaecoll - About J. Holstein SMNS-E-araneaecoll - BPS (-) GBIF doi:10.15468/dehmye GFBio 4.423 (4.364) unit based {2018-09-10} -
SMNS-Z-herpcoll - About A. Kupfer SMNS-Z-herpcoll - BPS (-) GBIF doi:10.15468/g6ggjy GFBio 13.450 (4.975) part based {2018-09-10} -
TUBvplantscoll - About C. Dilger-Endrulat TUBvplantscoll - BPS (+) GBIF doi:10.15468/2wbxxh - 9.008 (1.355) unit based {2018-09-10} -

 

SNSB Hosted IBF Datasources#

Datasource Description Data Curators BPS Local Query Tool (+/- UnitGUID of SNSB id service) Datasource Access in GBIF GBIF DOI Datasource Access in GFBio DC Master (Internal Access): IdentifUnits/UnitParts (GeorefUnits) {date} Specific Features
IBFfungicoll About J. Simmel, K. Bensch IBFfungicoll - BPS (+) GBIF doi:10.15468/8t1k88 GFBio 1.545 (1.015) unit based {2018-09-10} Monitoring, DGfMnames, LIASnames, TaxRef_LIAS_Erys_DE, BfNnames
IBFgallscoll About A. Guhr, G. Rambold IBFgallscoll - BPS (+) GBIF doi:10.15468/mxvyfi - 2.029 (1.895) unit based {2018-09-10} Monitoring, TaxRef_UBT_Galls_DE, BfNnames
IBFlichenscoll About W. von Brackel IBFlichenscoll - BPS (+) GBIF doi:10.15468/hs6htt GFBio 5.115 (3.679) unit based {2018-09-10} Monitoring, TaxRef_LIAS_Lichens_DE , TaxRef_LIAS_LichFungi_DE, LIASnames, BfNnames
IBForthopteracoll About H. Schott IBForthopteracoll - BPS (+) GBIF doi:10.15468/0hkfpf GFBio 101 (68) unit based {2018-09-10} Monitoring, TaxRef_SNSB_Orthoptera_DE
IBFplantscoll About W. Ahlmer, J. Klotz IBFplantscoll - BPS (+) GBIF doi:10.15468/2l5qts GFBio 221.051 (198.156) unit based {2018-09-10} Monitoring, BfNnames

Note 1 for scientific data curators:

The whole data pipeline starting from productive master databases until publication of datasets is under responsibility of scientific data curator(s):

Please test the BPS representation:

  • CLICK on the NAME of the DATASOURCE under the column BPS Local Query Tool above and find several options to manage data of the mapping and to view raw XML for extended information on the mapping of the datasource.
  • SELECT the option QUERY under "useful links" to test a selection of core data mapped.
  • SELECT a GROUP RESULT option as "scientific name", "country" and "locality" and use the SEARCH button.
  • TEST for inconsistencies concerning the identifications of the single units and whether data records which are to be retained are flagged out as withhold in the productive DiversityCollection databases and DiversityCollection_Monitoring databases.
  • ADD and IMPROUVE data by using .Net Clients and your personal account to the DWB databases, especially DiversityCollection installed at the SNSB IT Center and at other data repositories, e.g. of Natural History Collections in Germany.

 


Note 2: The delivery of the datasets via BioCASe is realised by a slightly different dataflow as used for the open access of data via cfm and jsp dataset-specific interfaces developped at the SNSB IT Center.


Note 3: Suggestions for citation (under development):

 

Alternative 1: Triebel, D. (2006 onwards). The Collection of Lichenicolous Fungi at the Botanische Staatssammlung München. – Accessed via http://www.botanischestaatssammlung.de/DatabaseClients/BSMlichfungicoll/DiversityCollection_BSMlichfungicoll_Find.cfm on 2016-xx-xx.

 

Alternative 2 for datasets published and accessed via GBIF

 

Holstein, J. (2015 onwards). The Spider Collection at the Staatliches Museum für Naturkunde Stuttgart. – Accessed via http://www.gbif.org/dataset/7a681cd5-9781-489f-a43b-dfd117967550 on 2016-xx-xx. Data publisher: Staatliche Naturwissenschaftliche Sammlungen Bayerns.doi:10.15468/dehmye.

Schott, H. (2013 onwards). IBF Monitoring of Orthoptera, University of Regensburg. – Accessed via http://www.gbif.org/dataset/6454fdd4-b62f-11e2-afcb-00145eb45e9a on 20xx-xx-xx. Data publisher: Staatliche Naturwissenschaftliche Sammlungen Bayerns. doi:10.15468/0hkfpf.

Triebel, D. (2007 onwards). The Collection of Lichenicolous Fungi at the Botanische Staatssammlung München. – Accessed via http://www.gbif.org/dataset/858c1c6c-f762-11e1-a439-00145eb45e9a on 2016-xx-xx. Data publisher: Staatliche Naturwissenschaftliche Sammlungen Bayerns. doi:10.15468/ni5yho.

 

Alternative 3 for datasets published and accessed via GFBio

see GFBio Consensus Document for citation pattern of ABCD datasets


 

some useful links:

GBIF Participants overview

GBIF Search data publishers

GBIF Voting participant Germany

GBIF Data publisher SNSB

GBIF Germany Data Summary

GBIF Publishing data

GBIF Citation guidelines

GBIF DOIs

GBIF data registry

GBIF data processing

GFBio search results for SNSB

GFBio VAT tool