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dara use constraints


 

All species occurrence datasets on GBIF.org now carry standardized licences, giving data users and publishers greater clarity and enabling them to proceed with confidence about the terms of use for data accessed through the GBIF network.

Built on a 2014 decision by GBIF's governing board, all occurrence datasets are now assigned one of the following three licences from Creative Commons:

  • CC0, under which data are made available for any use without restriction or particular requirements on the part of users
  • CC BY, under which data are made available for any use provided that attribution is appropriately given for the sources of data used
  • CC BY-NC, under which data are made available for any use provided that attribution is appropriately given and provided the use is not for commercial purposes

The vast majority of publishers (83%) have selected CC BY licences for their datasets, with CC0 licenses accounting for another 5 per cent. More info about this process at: http://www.gbif.org/newsroom/news/data-licensing-milestone

Check the following document to choose a license for your dataset (in Spanish): http://www.gbif.es/ficheros/infografia-Licencias.pdf

For more information on licenses watch these videos:

   
agreements


All the original agreements related with data sharing and use are available in GBIF Secretariat web portal, in the following address:
http://www.gbif.org/disclaimer/datasharing

 
GBIF Data Use Agreement

All the potentials users of GBIF data must read and understand the GBIF Data Use Agreement before being allowed to access data. In the following document, both Spanish and English versions of this agreement are included:
GBIF Data Use Agreement - English

 
GBIF Data Sharing Agreement

Before sharing any data in GBIF network, potential data providers must read and agree with GBIF Data Sharing Agreement. In the following document, both Spanish and English versions of this agreement are included:
GBIF Sharing Data Agreement- English

 
 
how to cite


As it is stated in GBIF Data Use Agreement, data users must acknowledge data providers and collections for their data as appropriate. In the following documents, different ways of meeting this requirement are discussed.

  • Guidelines for citing specimen and observation data obtained via the GBIF Data Portal - Spanish & English - PDF file (60 Kb)
  • Guidelines for citing names data obtained via the GBIF Portal - Spanish & English - PDF file (60 Kb)
  • How to cite GBIF data - White paper - Spanish & English - PDF file (168 Kb)

Use the following format to cite data retrieved from the GBIF network:
Biodiversity occurrence data published by: (Accessed through GBIF Data Portal, data.gbif.org, YYYY-MM-DD)

For example:
Biodiversity occurrence data published by: Field Museum of Natural History, Museum of Vertebrate Zoology, University of Washington Burke Museum, and University of Turku (Accessed through GBIF Data Portal, data.gbif.org, 2007-02-22)


 
   

To ensure interoperability when consulting different biodiversity databases spread around the world, it is essential to have standard datasets for natural history collections and observational databases. There are -at the moment- two main alternatives in this field:

 Darwin Core

What is Darwin Core? The Darwin Core is body of standards developed and promoted by the Biodiversity Information Standards (TDWG). It includes a glossary of TERMS (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information.

The Simple Darwin Core is a predefined subset of the terms that have common use across a wide variety of biodiversity applications. The terms used in the Simple Darwin Core are those that are found at the cross-section of taxonomic names, places, and events that document biological occurrences on the planet. The two driving principles are simplicity and flexibility.

Here you can download the Simple Darwin Core table in MS Access.

The version of the Darwin Core standard that is currently implemented by GBIF is the Darwin Core 1.2 (Classic) and Darwin Core 1.4. For a quick reference for mappings between elements in pre-standard Darwin Core versions and the current Darwin Core (Darwin Core 1.4 Paleontology extension) terms see Mapping Darwin Core to Old Versions.

The preferred format for publishing data to the GBIF network is the Darwin Core Archive (DwC-A), which is essentially a set of text (e.g., TAB or CSV) files with a simple descriptor to inform others how your files are organized. The format is defined in the Darwin Core text guidelines. It is already being implemented and will be supported by all the software application developed by the Coordination Unit.

ABCD

The Access to Biological Collections Data (ABCD) Schema is an evolving comprehensive standard for the access to and exchange of data about specimens and observations. This schema was developed within the BioCASe European project. It is a complex schema with nearly 1500 concepts/fields. Version 1.2 is currently in use with the GBIF (Global Biodiversity Information Facility) and BioCASE (Biological Collection Access Service for Europe) networks. To obtain further information about this standard, please visit:

Plinian Core

Plinian Core is a standard for sharing information mainly at the species level. It was conceived as a way to publish species information and to make it interoperable. By “species information” we refer to all kinds of properties and traits related to taxa (of any rank), including descriptions, nomenclature, conservation status, management, natural history, etc. Thus, Plinian Core coverage goes beyond taxonomic descriptions.

Difuminado de coordenadas

Licencia de Creative Commons
Logo Plinian Core by Humboldt Instituto de Investigación de Recursos Biológicos Alexander von Humboldt.
Created from https://github.com/PlinianCore/Documentation/tree/master/Logo-Pliniancore

 Scientific Names

Following these links you will find names lists to check the names included in your databases.

Specific groups:

Animals in general   Index to Organism Names (ION)
Mammals   Mammal Species of the World (MSW)
Birds   AviBase
Fish   FishBase
Amphibians   Amphibian Species of the World (ASW)
Vascular plants   International Plant Names Index (IPNI), TROPICOS, the Plant List.
Mosses   Most and also: Index to Organism Names (ION)
Fungi and lichens   CABI and also: Index to Organism Names (ION)
Algae   AlgaeBase, Index Nominum Algarum and also: Index to Organism Names (ION)
Bacteria   List of Bacteria with Standing in Nomenclature (LBSN)
Virus   The Universal Virus Database of the International Committee on Taxonomy of Viruses (ICTVdB)

Taxon Checklist of Vascular Plants from Spain

This is a curated checklist of all vascular plants reported in Spain. It contains 10,493 taxa covering 212 families, 1,399 genera, 7,069 species and 1,813 subspecies and can be downloaded as a Darwin Core file. For every taxa, names and bibliographic references a LSID is provided. Flora iberica is the main source of classification as well as Anthos project. This database have been released to the public domain under a CC-BY license and is available through the IPT of GBIF Spain at http://www.gbif.es/ipt/resource?r=taxonesfloraespanola.

Plant names in Spain with LSIDs for biodiversity information systems and data sharing

The following databases provide users with a list of scientific names extracted from The International Plant Names Index (IPNI) for plant genera by selecting names of those plants covered by the Anthos project. This catalogue contains more than a half a million plant names, all of them with permanent identifiers (LSIDs). The information is provided in two formats, both are compatible with some of the applications developed by the Coordination Unit of GBIF.ES, allowing databases to be handled as dictionary of names.

  1. NOMEN format compatible with Herbar, Zoorbar, HZL y BIBMASTER. (MS Access and txt)
  2. Species2000 format compatible with Darwin Test. (MS Access and txt)
 
Fields and properties
Downloads
NOMEN Format
NOMEN Structure (.pdf; 64 Kb)
MS Access (.rar; 32.8 Mb)
Text (.rar; 18 Mb)
Species2000 Format
MS Access (.rar; 20.6 Mb)
Text (.rar; 10 Mb)

 

In both cases, taxonomic hierarchy is included for each scientific name (Kingdom, Class and Order) using the Catalogue of Life/Species2000 database. This hierarchy has been lately revised following these taxonomic classifications:

Ferns:
Smith, A.R. et al. (2006). A classification for extant ferns. Taxon 55(3): 705-731.

Gymnosperms:
Christenhusz, M.J.M. et al. (2011). A new classification and linear sequence of extant gymnosperms. Phytotaxa 19: 55-70.

Angiosperms:
APG III (2009). Bot. J. Linn. Soc. 161:105-121.

This work has been made with the great collaboration of Miguel Ángel García from the Iberian Flora project.

Important notes:

  • The information of the fields referred to the scientific publication may contain truncated values, i.e. incomplete texts.
  • In both cases databases are provided in MS Access 2007/2010 as older versions of MS Access cannot handle a large number of records.
  • Sometimes a unique name may have different LSIDs. In these cases we have kept IPNI's classification although it would be better to delete homonyms when the database is used as a dictionary of names. Homonyms are saved in the field HasHomonyms. Besides, species from homonyms genera are distinguished with the text “Species of an homonym genus” in the Nomenclatural Remarks (Format Species2000) or Observnom (Format NOMEN) fields.
 
 
  • Catalogue of Life: gateway to our database of the world's known species of animals, plants, fungi and micro-organisms.
  • Index Herbariorum: a global directory of public Herbaria and associated staff.
  • Plant Systematics: includes the authors of plant names, providing the standard abbreviations.
 
 
software


The Coordination Unit of GBIF Spain develops software applications, freely and openly offered to the Spanish scientific community to facilitate data sharing through GBIF initiative. Software support and training is also offered freely to those researchers actively participating in GBIF.

 
Technical support to users of the applications developed by the Coordination Unit
 

The Coordination Unit offers free technical support to the users of the GBIF software to solve problems of installation and other issues regarding the use of the informatic applications. Assistance on version migration and update processes is also possible.

The active participation of users is very important for the process of software development, so suggestions are very welcome. These suggestions are studied and included in the next version when they have a sufficient demand, and it is technically possible.

To request technical support for these informatic tools you can contact the Coordination Unit at info@gbif.es

 
Software of Collections and Projects management
 
When tackling a digitization process of a natural history collection, observational data obtained in the field,literature data or any other biodiversity data source, it is essential to know the tools available to carry out the task in an effective way.

Joining an existing well-known initiative ensures taking advantage of the expertise acquired by other research groups, making easy to avoid known problems. A smooth and effective performance of the digitization works becomes possible then, from the very beginning of the project. The most recent international standards in biological databases are surely covered, as it is sharing information between different databases, facilitating joining global initiatives like GBIF.

 
 ELYSIA: Natural history collections management

Logo Elysia   

ELYSIA is the new application software to digitize and manage botanical and zoological natural history collections developed by the GBIF Spanish Node. Elysia is the result of merging Zoorbar and Herbar tools, which developments have now been suspended. Elysia includes all of their functionalities and other new ones as: generating universally unique identifiers for specimens (UUID), export process to Darwin Core Archive format and support to implement the Nagoya Protocol. Elysia is a Microsoft Access based program.

Please find further information about ELYSIA in its website (only in Spanish):

http://www.gbif.es/elysia/elysia.php

 
 HERBAR: Botanical collections management program

Herbar Logo   

HERBAR is a computer application designed to manage and digitalize botanical collections. It is a very complete program, and it's supported and recommended by the GBIF Spanish Node.

It is the standard application of the Iberian and Macaronesian Herbarium Association - AHIM (Asociación de Herbarios Ibero-macaronésicos) and it is regularly used in dozens of Spanish institutions to manage herbaria and seed banks.

Please find further information about HERBAR in its website:

http://www.gbif.es/herbar/herbar_in.php

 
 ZOORBAR: Natural history collections management program
Zoorbar Logo   


ZOORBAR
is a piece of software to digitalize and manage natural history collections developed and recommended by the Spanish GBIF Node. Its flexible attribute system makes possible to adapt it to any biological collection.

This program is having an interesting introduction into the zoological community in Spain, and several significant institutions are already managing their collections with ZOORBAR.

Please find further information about ZOORBAR in its website:

http://www.gbif.es/zoorbar/zoorbar_in.php

 
 HERBAR-ZOORBAR LIGERO: Biological collections management program
Logo HZL   


Herbar-Zoorbar Ligero
is a computer application designed to manage and digitalize either Botanical Collections or Zoological Collections. Its main goal is making the data exchange easier by using fast recording tables so, it is not neccesary to work with the complete versions of Zoorbar or Herbar.

Please find further information (in Spanish) about HZL on the following link:

http://www.gbif.es/hzl/hzl.php

 
 BIBMASTER: Biodiversity Information Manager

Bibmaster Logo   

BIBMASTER is a database application to manage biodiversity information, specially focused in bibliography and nomenclatural information. It is developed and recommended by the Spanish GBIF Node.

This program can manage nomenclature, literature, specimen and taxon level information: reference lists, key-words, nomenclature, iconography, check-lists, specimen-lists, herbarium labels and much more.

Several relevant national initiatives use BIBMASTER to manage information, like Flora iberica or Flora Micológica Ibérica projects.

Please find further information about BIBMASTER in its website:

http://www.gbif.es/bibmaster/bibmaster_in.php

Other sowftware

You can check a complete list of software for digitizing natural history collections in the web pages of the TDWG Subgroup on Biological Collection Data. There you will find links to programs like HERBAR, SPECIFY, BIOTICA, RECORDER2000 and so on.
 
Software of Validation and Transformation
 FindIt2DarwinCore
 
logo fin it   

FindIt2DarwinCore is a software designed to extract scientific names stored in PDF documents located on a web address, entering data into a table with Darwincore format. This application uses the "FindIT" web service located at www.ubio.org and can be downloaded at:

http://sourceforge.net/projects/findit2darwinco/

This software has been developed in collaboration with the UBIO staff.

     
 
 DARWIN TEST
 
Darwin Test   

DARWIN TEST is a software application to validate and Darwin Core records (Darwin Core 1.2, Darwin Core version 1.4 or Darwin Core Archive), standard to facilitate the sharing of information about biological diversity.

Before publishing your biodiversity data in a public network such as GBIF it is highly recommended to test your data using DARWIN TEST in order to detect possible problems. The issues analyzed include omission, typographic, convention and coherence errors. DARWIN TEST is a Microsoft Access based program. The software is available also in English.

Please find further information about DARWIN TEST in its website:

http://www.gbif.es/darwin_test/Darwin_Test_in.php

 
Name Parser
 
Name Parser   

NAME PARSER

MS Access 2000® application to parse scientific names into their components: genus, species, species author, Infraspecific rank, Infraspecific Epithet, infraspecific author and year.

Please find further information about NAME PARSER in its website (in Spanish):

http://www.gbif.es/name_parser/Name_Parser.php

 
More digitalizing software

There are plenty of initiatives in the software development field to manage and use biodiversity information. Some examples are shown in the following sections:
 
 VegAna from the University of Barcelona


Logo VegAnaThe Botany Unit from the University of Barcelona has developed an integrated software package called VegAna (Vegetation Edition and Analysis) to manage and analyse biological data . You can download the following applications from the project's main webpage:

  • ZamiaDroid: data capture with mobile devices.
  • Ginkgo: representation, classification and multivariate analysis of biodiversity data.
  • Quercus: relevé data tables editor. Handles relevé data to perform phytosociological works.
  • Fagus: floristic citation editor.
  • Yucca: a cartographic plotting tool.

A new fascinating function has been added recently to this software: GBIF data import and use!

To find further information, please visit B-VegAna webpage:

http://biodiver.bio.ub.es/vegana/index.html

 
DEMIURGE
 

Logo VegAnaThe Jardín Botánico Canario “Viera y Clavijo” – Unidad Asociada CSIC (Cabildo de Gran Canaria), the Instituto Tecnológico de Canarias (Gobierno de Canarias), Mr. Bicho, The Agile Monkeys, Claudesign, and the Fundación Amurga-Maspalomas are developing DEMIURGE, an enhancer of knowledge on biodiversity’s genetic diversity that follows GBIF standards of data interchange and structure. Demiurge is a free-access, searchable public repository of genetic diversity digests (i. e., geo-referenced genotype matrices plus ancillary information relevant to their interpretation) that will facilitate a versatile statistical analysis and meta-analysis of genetic data through the genetic information standards provided by the associated software Transformer-4 (T4). These deliverables originate from activities of the project DEMIURGO co-funded by the Programa de Cooperación Transnacional Madeira-Açores-Canarias (FEDER), the Jardín Botánico Canario “Viera y Clavijo” – Unidad Asociada CSIC, and the Instituto Tecnológico de Canarias.

For further information on the progress of Demiurge go to:

http://www.demiurge-project.org/

 
 ModestR
 

ModestR is a software tool aimed to provide academic community (particularly people involved in Ecology and biodiversity management) with a powerful but easy-to-use tool for working with species distribution maps and taxonomic data. ModestR is made up of three main applications: MapMaker, DataManager and MRFinder.

MapMaker provides an intuitive and very easy GIS-like environment to build species distribution maps. It has been designed around the concept of habitats, allowing the user to build range maps as easily as if he/she were drawing, with tools like freehand to select areas and choose which habitats of this area are occupied by a species. MapMaker will only fill the selected habitat, providing immediately a visual impression of the real areas occupied by a species. Currently five different habitats are supported: sea, land, large river areas, small river areas, and lentic waters.

DataManager is an application that allows users to create their own ModestR databases with taxonomic and species distribution information. A Modest database consists of a taxonomic tree that can be populated manually or directly imported from CSV data or from another ModestR database. Once entered taxonomic data, maps built with MapMaker, imported from CSV files or downloaded from GBIF (among other possibilities) can be stored linked to species in the database. This way, taxonomic and distribution data can be easily managed together. DataManager offers several options to export data from database like taxonomic data, presence data from a species, or richness data from any taxonomic group.

MRFinder allows to fully take advantage of the data stored in a ModestR database. With MRFInder you can find which species are present in specific areas of the world, just by selecting those areas as a rectangles or irregular polygons in the map. MRFinder supports using predefined selections that can be imported from existing shapefiles or KML. That makes easy importing administrative maps and using them as templates to search for species.

ModestR runs on Microsoft Windows XP/Vista/7/8 64bits version.

ModestR is available at: http://www.ipez.es/ModestR/

 
 GBIF Integrated Publishing ToolKit (IPT)
 

The GBIF Integrated Publishing Toolkit (IPT) is a free open source software tool written in Java that is used to publish and share biodiversity datasets through the GBIF network. The new IPT offers simple interfaces to transfer complete data stores in order to publish biodiversity data. The core development of the IPT happens at the GBIF Secretariat, but the coding, documentation, and internationalization are a community effort and everyone is welcome to join in.

All information related to IPT at: http://www.gbif.org/ipt

Find detailed technical information including download and installation guidelines at https://code.google.com/p/gbif-providertoolkit/

Spanish IPT: http://www.gbif.es:8080/ipt/

 
 
 
  
  
Digital Images


Modern methods to digitalize natural history collections and to increase the value of the collections and the databases behind them include specimen digital image capturing.

Digital image use offers many ADVANTAGES:

  1. Herbarium sheetThey are easy to manipulate and distribute: computer files are readily transported and stored in CD, DVDs or through the Internet.
     
  2. Disaggregation of collections' digitalization process. It is no longer necessary to complete all the digitalization effort in the collection site or to carry the specimens: image capturing can be done within the collection and processed elsewhere.
     
  3. Great amounts of information can be accessed with no need to travel to the collection site or to handle the specimens. A lot of research can be done using digital images, avoiding the cost and risk of damaging delicate specimens associated with loans and transportations. This point is especially important regarding delicate or unique type material.
     
  4. The Collections' curator and staff are released from most of the tasks related with loans and queries. This time can be invested in better curation or research.
     
  5. Researchers save the time needed to go to the collections site to check specimens' features perceptible in the digital image.
     
  6. The data (labels, identifications) and databases associated with the collections can be corrected and updated based on the information provided by the digital images of the specimens and their labels.
     
  7. High quality data sharing with countries of origin (data repatriation) is facilitated, providing them with 'virtual collections' built from the specimens collected in their territories.
     
  8. And so on.
 

Some of the most interesting international initiatives are listed below. These ones are remarkable because of their significance or their special characteristics:

E-Type Initiative

This ambitious initiative from Harvard College is attempting to create a web-accessible electronic catalogue of all type specimens to be used by all taxonomists and specialists around the world. They maintain a complete online guide about digitalization and image capture of diagnostic characteristics.

The first results of this effort can be consulted in the online catalogues of their Caribbean insects collection and the type specimens of the MCZ collection.

New York Botanical Garden

The New York Botanical Garden is one of the pioneer institutions in everything related to digital herbaria creation and access. About 800,000 digitalized specimens are available at the moment, with more than 120,000 high resolution images and its own search engine.

Zoological Museum Amsterdam

The Zoological Museum of Amsterdam, in collaboration with the National GBIF Node of Holland, and with the technical support of ETI Bioinformatics, has developed a project of types specimens digitalization in three dimensions (3D), whose first results -a birds collection- can be queried online. This innovative system allows to rotate the specimen and to view it under any desired angle.

Center for Biodiversity and Conservation

The Center for Biodiversity and Conservation belongs to the American Museum of Natural History. Its mission is to mitigate critical threats to global biological and cultural diversity by advancing scientific research in diverse ecosystems; strengthening the application of science to conservation practice and public policy; developing professional, institutional, and community capacity; and furthering the Museum's efforts to heighten public understanding and stewardship of biodiversity.

Aluka

Aluka is an international, collaborative initiative building an online digital library of scholarly resources from and about Africa. Start-up funding for Aluka has been provided by The Andrew W. Mellon Foundation. Aluka seeks to attract high-quality scholarly content about Africa from institutions and individuals across the globe. By contributing their collections to the Aluka platform, content owners will have a means of offering access to their collections to an international audience—without having to develop and support their own technology platforms.

 

Furthermore, there are additional global initiatives to capture digital images in natural history collections: some of them are really significant, like the project of Linnean Types Herbarium digitalization.


There are also several Spanish initiatives working in the same direction:

   
 
GBIF and Digital image use

GBIF International data portal shows digital images of some taxa, with the collaboration of several institutions like the Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM) and the University of Zürich Herbarium (Z+ZT).

The Coordination Unit of GBIF Spain offers to the Spanish data providers its Hosting and Publishing Service of high resoluction images. Some examples of collections that own high resolution images that are hosted and accesible at the GBIF.ES can be visited here.

 
 
Methodology

Here they are some resources to check when proposing or facing projects with a specimen digital image component:
  1. ENBI Manual Front PageThe EUROPEAN NETWORK FOR BIODIVERSITY INFORMATION (ENBI) included different initiatives related to the use of digital imaging of natural history collection specimens in its 6th work package (Co-operation of pan-European databases on biological collections and specimens). Some of the most interesting related events are:
     
    • A workshop on 'techniques and challenges for digital imaging of biological types' was held in Stuttgart (Germany) in March 2004.
       
    • A 'Manual of Best Practice' on digital imaging of biological type specimens was published at the end of 2005. Among the contributions included in this manual, the Spanish study of Arturo H. Ariño and David Galicia on the use of digital images in taxonomical studies stands out (Chapter 11th). A full electronic version of the manual is available to download here.
       
  2. A working group focused on biological images management has been established in the TAXONOMIC DATABASE WORKING GROUP (TDWG). They have launched a WiKi as a discussion and focal point, where new ideas as also published.
     
  3. The NEW YORK BOTANICAL GARDEN has made a manual on 'Procedures and recommendations for photographing and archiving type specimens of the New York Botanical Garden Herbarium' available. It includes different recommendations about the equipment needed, its configuration, lighting control, etc.
     
  4. The E-TYPE INITIATIVE web pages also include some information about protocols, considerations and methodology, when facing detailed images capturing.
     
  5. The COORDINATION UNIT OF THE SPANISH GBIF NODE organizes periodic courses and workshops on Digital Image for Biodiversity Studies, whose contents include the process of capture, management and Internet publication of digital images of natural history collection specimens and other images related to biodiversity research projects: icons, microscope slides, etc.. Please visit the training and outreach section of GBIF.ES web portal to be properly informed about future calls.
  
 
Sensitive Data
 
 Definition


Data generalizationThe concept of SENSITIVE DATA in the context of GBIF refers to those data about taxa whose geographical information publication could be problematic if shared unprotected. This situation can occur when publishing information about:

  • Rare, endangered or legally protected taxa.
     
  • Commercially valuable taxa.
     
  • Showy or fragile taxa (Ex: orchids, nesting/roosting sites, etc.).
     
  • Data subject to withholding request from landowner.
     
  • Data used to derive income.

In other context, there is data that can be considered "temporarily" sensitive:

  • Data awaiting publication.
     
  • Data subject to ongoing research.

The concept of sensitive data, like those of endemicity or rareness, is closely related to the geographic area we are restricted to: data considered as sensitive in a given area, can be considered freely accessible in a different one. This is particularly relevant when talking about duplicates of vouchered specimens stored in different natural history collections, or data served from outside the influence area of the restriction, legislation, etc.

 
 Sensitive data sharing in GBIF


When facing the possibility of sharing sensitive data through the GBIF network, a geographical data generalization or deletion process must be conceived and run, before their publication.

One of the most relevant issues which can't be neglected when sharing sensitive data is to document the process carried out to generalize or remove the geographical information. Users must be aware that the data made available for them is not the original data. Nevertheless, the generalized data available in the internet will inform users of its existence and data providers can keep the capacity to evaluate individually the convenience of sharing more detailed information.

 
 How to manage these data?


The FIRST STEP is to find out which records of our set are considered sensitive in our scope. Speaking about Spain, it is essential to know the applicable international, national and regional legislation:

European environmental legislationInternational Legislation

National Legislation

Regional Legislation

The SECOND STEP to take is to decide which method of protection we want to apply to the records:

  1. Totally remove geographical information: affecting both the textual description of the locality and the geographical coordinates (if available) of the collecting site.
     
  2. Partially remove the geographical information. Several methods are available:
    1. Round-down coordinates to a given number of decimal figures (Ex: use squares which define an area of 10x10 Km).
    2. Remove the contents of the most detailed fields of the locality (Ex: keep only the information about the country, state/province or municipality).
       
  3. Generalize geographical data: Original accuracy is maintained but the point does not match the original collecting/sighting site. Tools to carry out these tasks automatically are being developed: once they are available, they will be published here.

FINALLY, as it has been stated at the beginning of this document, it is essential to clearly indicate in a field ('notes' or a similar one) the process the records have undergone. Typical signs might read:

  • This specimen represents an endangered or threatened species. The specific locality has been removed from the on-line record to protect this species from over-collection. These data may be supplied to researchers on request.
     
  • This specimen represents an endangered or threatened species. The specific locality has been generalized to presence within a grid 1 minute resolution. Detailed data may be supplied to researchers on request.
 
 Sensitive Data Management Workshops


The Coordination Unit of the Spanish GBIF Node organised the first call of the Sensitive Data Management Workshop in 2008. In the framework of publishing sensitive data on line, restrictions arise mainly from the protection of endangered/legally protected species and from the safeguard of due attribution for the owner of data. Without minimizing the importance of the second issue, the workshop was focused on the first one: the protection of threatened species by means of the restrictive access to sensitive data. In 2012 we offered the same course online.

Find further information (in Spanish) about the workshops on: http://www.gbif.es/formaciondetalles.php?IDForm=44 and http://elearning.gbif.es/AContent/home/course/content.php?_cid=194

 
 Available Documents


If you are interested in obtaining more information, GBIF Secretariat in Copenhagen has issued several interesting documents related to sensitive data:

  1. GBIF Surveys in SurveyMonkeyIn March 2006, a survey was carried out to evaluate what was considered sensitive data by biodiversity data providers, and the methods used to tackle the management of this kind of information. There is a report on the results of this survey in:

    Questionnaire on Dealing with Sensitive Primary Species Occurrence Data (.PDF file, 567 Kb).
      
  2. When the analysis of the survey was finished and after having studied other similar initiatives, a complete report about dealing with Sensitive Primary Species Occurrence Data was made available.

    Report - Dealing with Sensitive Data (.PDF file, 530 Kb).
      
  3. The final step in this process was to develop a Guide to Best Practices. This document should be seen as an overriding guideline for institutions, data providers and GBIF Nodes to use to develop their own in-house guidelines.

    Guide to best practices for generalising primary species occurrence data (.PDF file, 558 Kb).
 

Español

GEOLocate

Traditional methods for georeferencing collection data (capturing map coordinates) from text descriptions are tedious and time consuming, typically involving finding the locality on either a hardcopy or digital maps, plotting the locality, and determining the coordinates.

GEOLocate is a comprehensive electronic georeferencing solution funded by the National Science Foundations and developed by Tulane University's Museum of Natural History designed to facilitate this task of assigning geographic coordinates to the locality data associated with natural history collections.

More information:

geolocate
geolocate

 Earth Point - Display grids on Google Earth

Earth Point provides a variety of tools for Google Earth. One of the features of Earth Point is to display grid systems on Google Earth. Lat/Lon, UTM, UPS, MGRS, USNG, and Georef are supported. As you zoom in the grids are redrawn at greater levels of detail. A paid user account is recommended although it is also possible to use a free version of the tool. You must have Google Earth installed to use this data.

http://www.earthpoint.us/Grids.aspx

 
Mapping tools
Tools to display geocoded records derived biodiversity data sources

Downloadable software:

   
  • C-squares mapper
    The CSIRO Marine Research (CMR) c-squares mapper is a perl utility. Latitutes and longitudes are converted to c-squares, which are georeferenced tiles (squares) representing identifiable portions of the earth's surface.
    Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia.

    http://www.marine.csiro.au/csquares/
CSIRO logo
  • DIVA-GIS
    DIVA-GIS is free geographic information system (GIS) software. It can be used to create species distribution maps and grid maps of the distribution of biological diversity as well as predictions of species presence based on climate using the BIOCLIM or DOMAIN models.

    Download: http://www.diva-gis.org/
Logo DIVA-GIS
  • gvSIG
    gvSIG is a tool oriented to manage geographic information. It is characterized by a user-friendly interface, with a quick access to the most usual raster and vector formats. In the same view it includes local as well as remote data through a WMS, WCS or WFS source.

Download: http://www.gvsig.com/

gvsig
  • Geobide Map
    Geobide Map es el componente de visualización de datos geográficos de la suite Geobide. Se caracteriza por su facilidad de utilización y su capacidad para acceder de forma ágil a múltiples fuentes de datos, vectoriales y ráster, y también a datos de servicios OGC (WMS, WFS). Contiene además una galería de mapas base personalizable que ofrece los más conocidos y utilizados (Google Maps, Bing, OpenStreetMap, ESRI…).

    Permite crear mapas profesionales de calidad y elaborar cartografía temática. Incorpora una potente herramienta para la generación automática de series cartográficas.

Descarga: http://www.geobide.es/geomap/

  • Google Earth
    Google Earth lets you fly anywhere on Earth to view satellite imagery, maps, terrain, 3D buildings and even explore galaxies in the Sky. You can explore rich geographical content, save your toured places and share with others.

Download: http://earth.google.com/intl/en_uk/

google earth
  • Google Maps
    Google Maps is a free web mapping service application and technology provided by Google that powers many map-based services including the Google Maps website, Google Ride Finder and embedded maps on third-party websites via the Google Maps API. It offers street maps, a route planner, and an urban business locator for numerous countries around the world.

Descarga: http://maps.google.com/

google maps

Online mapping applications:
   
Logo Canada
logo geo:truc
 
Geographic and species distribution tools

GEOSS

Displaying the position of a site geographically can help to detect errors and therefore to increase data quality. Some of these tools -known as geographic information systems (GIS)- also contain analytical functions which make possible the prediction of species' distribution.

GEOSS LogoOne of the most relevant international initiatives in development nowadays is GEOSS, the Global Earth Observation System of Systems. It is envisioned as a large national and international cooperative effort to bring together existing and new hardware and software, making it all compatible in order to supply data and information at no cost. It is coordinated by the Environmental Protection Agency of the United States.

GEOSS can be considered as a counterpart of GBIF in the geographic information field. It is due to become a key element that will make possible impressive advances in the analysis and use of biodiversity information, as it will make tools and big datasets available for big-scale studies.

 

GEOTeca

The GEOteca web site hosts a compendium of geographic resources compiled by students and lecturers of the University Autónoma de Madrid within the framework of Programas de Inovación Docente.

It gathers geographical information that can be found on the Internet in its widest sense:

  • Digital publications on geography and environment, degrees, departments, societies and literature.
  • Spanish GIS services available via Internet and international resources.
  • Satellite imagery relevant to Spain, image processing software etc.
  • Server on statistical population data, local, regional, national and international data, products and natural resources, documentation, literature, etc.

Their webpage: http://www.uam.es/docencia/geoteca/geoteca.html

geoteca
 
Data and structures for data migration

When performing data migrations, its essential to attach our data to an internationally accepted coding to ensure compatibility with global initiatives and subsequent data exchanges.

  1. ISO 3166 code lists: codes and names from ISO 3166-1 (the country codes) and ISO 3166-2 (the country subdivision codes) in English and French.
      
  2. MS Access® countries table with ISO 3166-1 codes of two and three characters length and its names in Spanish: Paises.zip (.ZIP file, 21 Kb - Last update 12-02-2007).
       
  3. Table with the codes of country subdivisions (states, departments, provinces,...) as they are defined in the ISO 3166-2 standard (60 countries): Provincias.zip (.ZIP file, 45 Kb).
     
  4. GADM database of Global Administrative Areas. GADM is a spatial database of the location of the world's administrative areas (or adminstrative boundaries) for use in GIS and similar software. Administrative areas in this database are countries and lower level subdivisions. The data are available as shapefile, ESRI geodatabase, RData, and Google Earth kmz format. Shapefiles can be used for most mapping and GIS software. You can download the data by country or for the whole whole world.
 
 
BioGeomancer Guide to Georeferencing

  

This publication is one of the outputs from the BioGeomancer project and discusses in depth best practices for georeferencing biological species (specimen and observational) data. The publication presents examples of how to georeference a wide range of different location types, and provides information and examples on how to determine the extent and maximum uncertainty distance for locations based on the information provided.

Released on: 22 August 2006

Written by: Arthur D. Chapman and John Wieczorek

Concerned URL: http://www.gbif.org/resources/2809

 
 
 Principles of Data Quality
  


Data quality
and errors in data are often neglected issues with environmental databases, modeling systems, GIS, decision support systems, etc. Too often, data are used uncritically without consideration of the errors contained within, and this can lead to erroneous results, misleading information, unwise environmental decisions and increased costs. This paper expands on these issues and discusses a number of principles of data quality that should become core to the business of the natural history collections and observational communities as they release their data to the broader community.

Released on: 17 August 2005

Written by: Arthur D. Chapman

Concerned URL: http://www.gbif.org/resources/2829

 
 
Principles and Methods of Data Cleaning

  

This document examines methods for preventing as well as detecting and cleaning errors in primary biological collections databases. It discusses guidelines, methodologies and tools that can assist the natural history collections community and the observational communities to follow best practice in digitizing, documenting and validating information. But first, it also sets out a set of simple principles that should be followed in any data cleaning exercises.

Released on: 17 August 2005

Written by: Arthur D. Chapman

Concerned URL: http://www.gbif.org/resources/2833

 
Uses of Primary Species-Occurrence Data
 
  

This paper examines uses for primary species occurrence data in research, education and in other areas of human endeavor, and provides examples from the literature of many of these uses. The paper examines not only data from labels, or from observational notes, but the data inherent in museum and herbarium collections themselves, which are long-term storage receptacles of information and data that are still largely untouched.

Released on: 17 August 2005

Written by: Arthur D. Chapman

Concerned URL: http://www.gbif.org/resources/2834

 
 
Guide to Best Practices for Generalising Sensitive Species Occurrence Data
 
  

This Guide to Best Practices for Generalising Sensitive Species Occurrence Data provides a key for data providers to use in determining whether a species or attribute should be regarded as sensitive and its level of sensitivity, and provides guidelines on consistent wording for use in documentation.  It also provides guidelines on methods for generalizing data, both spatial and non-spatial.

Released on: 31 March 2008

Written by: Arthur Chapman and Oliver Grafton.

Concerned URL: http://www.gbif.org/resources/2760

 
 
Significance of Organism Observations
 
  

Observations of nature are the foundation of ecological studies, which use observations to search for patterns in nature, and biodiversity conservation. Organism observations (observational) data is a major constituent of “primary biodiversity data”.

Released on: 09 October 2008

Written by: Steve Kelling.

Concerned URL: http://www.gbif.org/resources/2761

 
 
Observations on observational biodiversity data
 
observations    

This publication describes all the work done for ENBI at the University of Turku.

Released on: 21 March 2006

Written by: J. Salo, M. Vieno, T. Toivonen, I. Saaksjarvi, R. Kumpulainen, S. Juvonen.

Concerned URL: http://enbi.utu.fi/Documents/lcc9_observations_on_obsdata%2B%2B.pdf

 
 
A view on collection databasing
 
razones   

Writter: Francisco Pando

Collection databasing is expensive and laborious, and their results are only visible in the long term. It is for that reason that such a task should be tackle from the perspective of the utility. When planning the computerization of a collection, is necessary to consider carefully the objectives and how the database is going to fulfill them. Doing otherwise is throwing away time and money.

From the experience acquired in collection databasing at our institution, we learnt that the most costly part of the computerization process is related to the transfer of the material between the herbarium and the computer, as much for the data entering as for data checking and proofreading. Therefore, it is more efficient to data enter everything for each specimen, for a limited amount of specimens (of a family, or a group of families, for instance) that to undertake a partial computerization of the whole collection. The computerization of a herbarium, must cover three objectives:

  • To contribute to exploit, in a more complete way, the information than the collection contains. This is especially desirable in the fields of the Ecology, Phenology, History, Nomenclature and environmental impact assessment.
  • To protect the specimens kept, by means of eliminating or reducing the need of manipulation of the material for many studies.
  • To contribute to the management of the herbarium in tasks such as labeling, loan processing (in and out) and exchanges.

One of the dangers when building a collection database occurs when the effort that supposes its accomplishment is disproportioned in relation to the obtained benefits. For this reason, it turns out to be especially interesting to bind the collection computerization to active research projects, which in some way need the information contained in the collection. In this way, the utility of the work is clear and its viability consolidates.

As in any database exercise, perspective on reality should no be lost. It is nonsense to make a database if the specimens are not well preserved. It is equally unsound to database a collection if the specimens cannot be found, or are not accessible. The priorities should be stated clearly: preserve, make accesible, database.

A practical detail, usually overlooked, is the relationship between database and collection. It is of the utmost importance to guarantee that going from the database to the specimen, and the other way around, is not only possible but straightforward as well. This goal implies two requirements: a) any specimen must be unmistakably identifiable from the data in the database, (i.e. with a database record at hand, the specimens it refers to can pinpointed exactly). Here is when accession numbers, barcodes and the alike enter in action. It is also most convenient to provide a system know quickly whether a specimen is already databased or not.The other requirement is that any specimen can be quickly located with the data in the database. (e.g. in multi- identification databases, which one is the specimen included under.

Finally, I would like to emphasize how vital is for the success of any collection database project is to integrate it in the routine of the collection. An important step in this direction is to persuade researches and collectors who contribute material to the collection to use a database compatible with the herbarium's for their own records list and labels. Conceiving collection databasing as an extraordinary action, limited in the time, implies that, when the collection grows, the database are not longer a representation of the collection, its utility drops, it loses interest, and eventually, is abandoned.

URL: http://www.gbif.es/videos/video_detall.php?IDVideo=53

 

 

  

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GBIF-ES is the Spanish node of the Global Biodiversity Information Facility
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by the Spanish National Research Council throught its
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