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). 53 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 14 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 processed 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 7.591 (7.147) part based {2018-09-10} | with images, stratigraphy, fossils |
| JMEfossilcoll - About | M. Ebert, C. Ifrim | JMEfossilcoll - BPS (+) | GBIF | doi:10.15468/*** | GFBio - Dataset, GFBio - Data Units | fossils | |
| SAPMmammaliacoll - About | H. Obermaier, N. Pöllath | SAPMmammaliacoll - BPS (+) | GBIF | doi:10.15468/elc2yx | GFBio - Dataset, GFBio - Data Units | 3.192 (79) part based {2018-09-10} | +- without images |
| SAPMpiscescoll - About | H. Obermaier, N. Pöllath | SAPMpiscescoll - BPS (+) | GBIF | doi:10.15468/uxag7k | GFBio - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 (+) | GBIF | doi.org/10.15468/thgjx1 | GFBio - Dataset, GFBio - Data Units | 7.131.680 (7.130.453) unit based {2018-10-16} | floristic record data from LfU survey studies for "Flora of Bavaria", verunschärft |
| BIOTAlichencoll - About | A. Beck, L. Zedda | BIOTAlichencoll - BPS (+) | GBIF | doi:10.15468/kosycz | GFBio - Dataset, GFBio - Data Units | 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 |
| GFBio201900216SNSB - About | T. Bruy | GFBio201900216SNSB - BPS (+) | GBIF | doi:10.15468/l8qg0g (GBIF) | GFBio - Dataset, GFBio - Data Units | 200 (200) unit based {2019-04-10} | 237 images, morphological data |
| GFBio201900230SNSB - About | M. Lauterbach, G. Kadereit | GFBio201900230SNSB - BPS (+) | GBIF | doi:10.15468/o21hxw (GBIF), doi:10.25897/5/5EPV-NZ13 (SNSB IT Center) | GFBio - Dataset, GFBio - Data Units | 26 (-) unit based {2019-08-07} | 26 images, morphological data |
| GFBio201900288SNSB - About | J. Wellsow, D.J. Harris | GFBio201900288SNSB - BPS (+) | GBIF | doi:10.15468/rfi78r (GBIF), doi:10.25897/5/2war-9p81 (SNSB IT Center) | GFBio - Dataset, GFBio - Data Units | 1.096 (854) unit based {2019-11-21} | |
| GFBio202300492SNSB - About | J. Firozpoor | GFBio202300492SNSB - BPS (+) | GBIF | doi:10.15468/ygzvjr (GBIF) | GFBio - Dataset, GFBio - Data Units | 500 unit based {2023-12-12} | |
| 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 - Dataset, GFBio - Data Units | 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 (alt) and GBIF | doi:10.15468/lxnnnf and doi:10.15468/7o2xuw | GFBio - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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) |
| SMNKbryocoll - About | R. Bussmann | SMNKbryocoll - BPS (-) | GBIF | doi:10.15468/xxx | - | 39.384 (?) unit based {2023-11-22} | - |
| 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 |
| SMNKlichenocoll - About | R. Bussmann | SMNKlichenocoll - BPS (-) | GBIF | doi:10.15468/xxx | - | 4.469 (?) unit based {2023-11-22} | - |
| SMNKphanerocoll - About | R. Bussmann | SMNKphanerocoll - BPS (-) | GBIF | doi:10.15468/xxx | - | 62.549 (?) unit based {2023-11-22} | - |
| SMNKspidercoll - About | H. Höfer | SMNKspidercoll - BPS (-) | GBIF | doi:10.15468/fmxx2i | GFBio - Dataset, GFBio - Data Units | 19.680 (17.645) unit based {2018-09-10} | with images |
| SMNKspiderstudcoll - About | H. Höfer | SMNKspiderstudcoll - BPS (-) | GBIF | doi:10.15468/pr26sz | GFBio - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 4.423 (4.364) unit based {2018-09-10} | with images |
| SMNS-Z-herpcoll - About | A. Kupfer | SMNS-Z-herpcoll - BPS (-) | GBIF | doi:10.15468/g6ggjy | GFBio - Dataset, GFBio - Data Units | 13.450 (4.975) part based {2018-09-10} | - |
| TUBvplantscoll - About | U. Grünert | TUBvplantscoll - BPS (+) | GBIF | doi:10.15468/2wbxxh | GFBio - Dataset, GFBio - Data Units | 8.793 (1.355) unit based {2022-07-22} | with images |
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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 - Dataset, GFBio - Data Units | 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 Voting participant Germany