There are two main mechanisms to invite users through the system. You can also use other external mechanisms to invite people, which lately is my preferred choice. As evident as it may sound, the first thing that we need to take into account is that whoever wants to join a group needs an account in the site. Depending on that, we have different options:

1. The 'Invite users' link in the left-hand menu inside the group. This option is only valid if the people you are targeting (1) already have accounts in the site, and (2) you have linked them as contacts/friends. A selection tool will appear with all your contacts so you can select the people you want to invite, and include a brief note explaining why you think they could be interested in joining the group.
    
2. The 'Invite friends' link in the FRIENDS/CONTACT section. This is a good option if the people you are targeting don't have accounts in the site and you want to automatically link them as contacts/friends once they become members. You need a list of email addresses and a text explaining why you think they could be interested in the group. As part of that text, you should clearly state the (1) URL of the site, (2) how to create an account on the site, (3) how to get to the group page, and (4) how to join the group.
    
3. Through an external mechanism. Sometimes good old email can do a very good job. You will probably have to describe the same procedures as in points 1 and 2.

For the third option, this is an example that I have recently used:

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[First, a brief paragraph describing the group and why we are inviting the person]

The group has now being created in the GBIF Community Site. If you are interested in joining the group and you are already a member of the site, please log in and then click on the link below to go to the group page:

http://community.gbif.org/pg/groups/XXX/

Once there, use the 'Join group' link in the left-hand menu to join the group.

If you are not member of the site, please go to the main page http://community.gbif.org/ and create an account using one of the options provided (regular, Yahoo or Google). Then you can click in the group page and follow the instructions above.

----------------------------

This brief explanation should be enough for most of the people, while they will still have your email in case they find trouble following the instructions.

Please share your experience inviting people to groups as comments to this blog post!

I would to work on GBIF data with my GIS. I would like to do some treatments like intersection, selection by attribute etc. for various species.

I tried to access to the data through the Web Service WFS, but it don't work. I used QGIS (I have this error message: "No Layers: Capabilities document contained no layers.") or PostGis. I tried different solution, fallowing advices on the GBIF website.

Does someone have a solution, or know why that doesn’t work?

Cheers, Onesime.

This is a compilation of recommendations by the members of the eLearning Guild in LinkedIn on how to record the best audio possible, for eLearning or any other purpose:

• First and foremost, look for the most quiet environment possible, far from conversations, opening doors, computers..., and without echo;
• Write a script and repeat it several times before the actual recording (it will avoid the 'uhmms'). Make sure that the main points come across, rather than say every word in the script;
• Stand if you can, your voice will sound more natural;
• Sound natural and conversational. Use your own words (without slang) and pronounce clearly. Make your pauses;
• Smile and keep a positive, animated, engaging attitude. Gesticulate as if in a normal conversation. The listeners will notice it;
• Bear in mind that you are addressing people: use a mirror or have someone in the room to listen to you. You can also ask questions (did you know that...?).
• Place your microphone to the side,  slightly higher than your nose and close to you to record directly your voice and not the reflections in the room walls. But not too close to avoid recording your breathing;
• Use a pop shield, if possible.
• Record preferably in the morning, when your voice is fresh;
• Drink water or eat an apple before the recording; and
• If you make a mistake, start the sentence from the beginning instead of re-record. Deleting sections in an audio file is one of the easiest post-recording editions you can make.

The Great Region, located between Rhine, Mosel, Sarre and Meuse, has a total area of 65.401 km2. Biogeographically, it is spread over the oceanic and continental zones.

The administrative complexity of the Great Region, four countries and five regional entities, offer a challenging opportunity for trans-boundary collaboration in terms of Nature Conservation. Since many years, administrations, scientists and naturalists gather primary biodiversity data that are crucial for science-based decisions making.

This website offers a trans-boundary view on species observations related to Birds and Habitats Directive, this project will deliver a more accurate evaluation of Natura2000 network. By linking nature monitoring, scientific research and innovation technology, it exposes publically funded data to a wider public and raises biodiversity loss awareness.

ABSTRACT

This report describes a case study where the Darwin Core RDF resource was loaded to the NCBO BioPortal. The objective of adding the Darwin Core RDF vocabulary to the NCBO BioPortal was to initiate the mapping and an evolving interoperability between the biodiversity data standards and the biomedical ontologies. The Darwin Core RDF resource declares a basic ontology with deliberately very limited declarations of relationship between the concepts. The Darwin Core RDF vocabulary can be seen as an OWL Full ontology and can be explored as such using the Protégé ontology management software tool.

INTRODUCTION

The NCBO BioPortal [1] provides a software platform for publishing ontologies used in biology and biomedical research. This platform was developed for sharing ontologies expressed using the web ontology language (OWL) (Noy et al., 2009; Whetzel et al., 2011).

Darwin Core provides a widely used vocabulary of terms and concepts for documentation of biodiversity information resources (Wieczorek et al., 2012). Darwin Core is ratified as a data standard by the Biodiversity Information Standards (TDWG) and well documented at [2] with a normative RDF representation available at [3].

The "Semantics of biodiversity workshop" [4] organized in May 2012 at Kansas University included participants from the Biodiversity Information Standards (TDWG) technical architecture group (TAG) and the Genomics Standards Consortium (GSC). This workshop proposed to establish a so-called "slice" in the NCBO BioPortal for Biodiversity KOS and ontology resources. Using the NCBO BioPortal was considered more appropriate and effective than an alternative implementation of a new and separate "Biodiversity Information Standards" BioPortal instance. Sharing Biodiversity ontologies with the Biomedical community is more efficient for cross-mapping and interoperability between these related domains of biology information resources. The "Semantics of biodiversity workshop" [4] has also introduced the development of an OWL ontology based on the Basic Formal Ontology (BFO) [5] for the Darwin Core terminology [6].

RESULTS

The original Darwin Core RDF vocabulary caused a “parsing error” message when loaded to BioPortal [7,8]. All concepts included in the Darwin Core are declared as properties (rdf:Property) or class concepts (rdfs:Class). The domain (rdfs:domain) or range (rdfs:range) was not declared for any of the Darwin Core concepts. The identification and removal of an undesired system character (byte-order-mark [BOM]) resulted in improved parsing when exploring the Darwin Core RDF vocabulary using Protégé, but the “parsing error” when loading to BioPortal remained. A new test including only a subset of the Darwin Core concepts replaced quote characters inside the XML nodes by html entities (") and parsed well when loaded to BioPortal. However when the complete list of Darwin Core concepts where loaded to BioPortal with the quote marks replaced in this manner the “parsing error” remained. A RDF/SKOS vocabulary with translations of the Darwin Core term descriptions was also loaded to BioPortal [9], but also caused “parsing error”.

A subset of the 10 first Darwin Core terms is parsing fine in the NCBO BioPortal, while a subset of the first 50 terms cause “parsing error”.

[1] http://bioportal.bioontology.org/

[2] http://rs.tdwg.org/dwc/terms/index.htm

[3] http://rs.tdwg.org/dwc/rdf/

[4] http://www.biocodecommons.org/workshops/sob.html

[5] http://bioportal.bioontology.org/virtual/1332

[6] not yet published

[7] http://bioportal.bioontology.org/projects/168

[8] http://bioportal.bioontology.org/virtual/3058

[9] http://bioportal.bioontology.org/virtual/3085

REFERENCES

Noy, N.F., N.H. Shah, P.L. Whetzel, B. Dai, M. Dorf, N. Griffith, C. Jonquet, D.L. Rubin, M.-A. Storey, C.G. Chute, M.A. and Musen (2009). BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research 37:170–173. doi:10.1093/nar/gkp440 PMCID: PMC2703982. Available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703982/

Whetzel, P.L., N.F. Noy, N.H. Shah, P.R. Alexander, C. Nyulas, T. Tudorache, and M.A. Musen (2011). BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Research 39:541–545. doi:10.1093/nar/gkr469. Available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125807/

Wieczorek, J., D. Bloom, R. Guralnick, S. Blum, M. Döring, R. De Giovanni, T. Robertson, and D. Vieglais (2012). Darwin Core: An Evolving Community-developed Biodiversity Data Standard. PLoS ONE 7 (1). doi:10.1371/journal.pone.0029715.

So I created a shape file with polygons using QGIS (my favorite GIS application) defining a one by one degree raster. This produces a shape file containing attributes for xmin, xmax, ymin and ymax values for each of the cells. Then I added another attribute column named "cellid" using the following formula in the attribute calculator:

cellid = 360 * (ymin + 90) + (xmin + 180) = (360 * ymin) + xmin + 32585

This will convert the coordinates of the lower left corner of a cell into the cellid.

Now, I have a nice shape file which can help me to quickly identify the cellid for any given cell. The picture below shows how this can be used in e.g. the Baltic Sea. The map is using a UTM projection, thus the cells are not rectangular here, but you can easily see, that Kiel Bight is mainly the same as cellid 52030.

So, if you want to know, if there are records for the bivalve Arctica islandica (Ocean quahog or Iceland cyprina) on Kiel Bight, you can just the GBIS web service like this:

http://data.gbif.org/ws/rest/occurrence/count?scientificname=Arctica+islandica&cellid=52030

As of today, this tells you there are 431 records. You can then list the records using:

http://data.gbif.org/ws/rest/occurrence/list?scientificname=Arctica+islandica&cellid=52030

Clicking on the first occurrence (http://data.gbif.org/occurrences/22268430), you will however find a location on land and not in the water. So there is something wrong here with the the location of the occurrence, but that is another story.

If you are interested in using this shape file, I have uploaded it here:

Shape file containing a vector grid for all cell ids used for the data web service

In this time, a test server have been set up and a company specialized in eLearning has been contracted to help us construct our first course. We are working with them at present to ensure that we take the most effective eLearning approach providing the nature of GBIF and the training initiatives we are already involved in.

The thematic area chosen for this first approach is biodiversity data quality and we will center our initial efforts in a eLearning course on georeferencing. This topic has been part of the GBIF training offer for quite a long time so there are plenty of resources available on the topic. It also includes many of the activities and capacities that the GBIF stakeholders deal with daily: location and use of internet resources and tools, biodiversity and geographical data management, metadata production and analysis, etc.

At the moment we are invited those interested in getting involved early in this process to join the biodiversity data quality interest group in the GBIF Community Site. The members of the group will have the opportunity to follow the project closer, test early prototypes, provide early feedback and influence the process. Join us if you are interested in the topic!!

Meanwhile, the GBIF Secretariat will work with the eLearning company a small group of experts with extensive experience in data quality issues to define and develop the initial contents of the course.

More info on this in June!

The result is a series of 12 introductory videos where they explain the basics of biodiversity data quality, data cleaning and fitness-for-use: some basic definitions, many good pieces of advice on ways to avoid the most frequent sources of error and lots of tricks to increase the quality and expand the use of existing digital data.

The videos are available as an album in Vimeo:

http://vimeo.com/album/1904479

And also linked to the GBIF Online Resource Centre (ORC):

http://www.gbif.org/orc/?sword=dqv&search_all=1&sortby=Title_Text&advanced_search=1

These videos will be part of the background, introductory material that we use in our eLearning course about data quality (I'll write another blog post on this soon). We are requesting feedback on these videos, as they are our first approach to this kind of training material. You can add your comments via Vimeo, the ORC or this post in the Community Site.

Below, you will find the first video as an example:
 

Short introduction to biodiversity data quality and fitness-for-use from GBIF on Vimeo.

Following up our EU nodes meeting, I just want to inform all of you about our Harmonia system.

Harmonia is an information system dedicated to alien species threatening native biodiversity in Belgium and in neighbour areas.

As I mention in my presentation, this system will soon be extented to the Netherlands, North of France and Luxembourg. The Belgian Forum on Invasive Species is the national node of the IUCN Invasive Species Specialist Group and of the NOBANIS network.

The resulting species list has been published on GBIF and I strongly encourage all other nodes to publish their own invasive cheklists. 

The environmental impact of non-native species is assessed in a standard, objective and transparent way through a simplified protocol developed by the Forum, the Invasive Species Environmental Impact Assessment (ISEIA) protocol. It consists of four sections matching the last steps of the invasion process, i.e. the potential for spreading and colonising natural habitats as well as the adverse impacts on native species and ecosystems. Scores for each section are assessed based on organism’s history of impact in neighbour areas together with their ecological profiles. More information about this protocol can be downloaded from here.

Should you have any questions about Harmonia, don't hesitate to contact me or Sonia Vanderhoeven who is in charge of Harmonia at the Belgian Biodiversity Platform.

Figure 1: The GBIF Vocabulary Server for development of Darwin Core extensions and controlled value vocabularies (code lists) based on the Terms and Concepts defined by the ratified and published Vocabularies of Terms.

Figure 2: The Darwin Core Archive provides a new archive format for efficient exchange of biodiversity datasets.

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[1] http://vocabularies.gbif.org/

[2] http://www.gbif.org/orc/?doc_id=2819&l=en

[3] http://rs.gbif.org/

[4] http://scratchpads.eu/

[5] http://vbrant.eu/content/wp4-standardisation