Hello, friends of the great multidisciplinary community #SteemSTEM and readers from all over the world. For this occasion I have prepared this article with the intention of demonstrating, once again, the importance of information technology for scientific research work. This time, the co-protagonist discipline will be biology, a beautiful science for which I felt a predilection during my high school studies and which -as I have said on another occasion- would have been the career I would study and practice in other circumstances of my life.

But let's leave the retrospective for another occasion. The topic in particular that will be developed in these lines has to do with the Global Biodiversity Information Facility (GBIF); an important resource that everyone who is dedicated to scientific research related to biology should know.

This first installment will address a bit what this system is, also referred to here as "service" and, in a later, will introduce another element that has caught my attention and inspired me for this series: the GBIF API, an interface through which programmers can develop client applications that interact with all the information compiled by this organization.

I must say that while writing this article I was surprised to discover that among the posts published and curated with the #steemstem tag, very few have had references to GBIF. In fact, in more than 18 thousand posts examined, I counted only 6 posts with the words "gbif", and of them only 2 were cases that had nothing to do with my publications! (By the way, in the future I will surely talk more about these programming for methodological issues like these).

Any contribution, suggestion or comment will be welcome, I hope you like it! 😄

Global Biodiversity Information Facility

All biology scholars are probably familiar with the term 'biodiversity', which actually refers to the notion of 'biological diversity', that is, the vast set of diverse living beings on planet Earth, organized through the cohabitation of individuals of different species in certain environments, thus shaping ecosystems. To speak of biodiversity is to imply processes such as evolution, genetic differentiation and many subfields of ecology, all scientific categories of biology.

But it can also mean talking about 'cultural biodiversity', as well as the marked - and hardly ignorable - influence of human beings on nature, with which they interact, sometimes beneficially and sometimes detrimentally. It should be remembered that biodiversity contributes to maintaining the ecological balance necessary for the survival of the human species, in addition to being extremely important for the production of food, medicines and diverse materials, becoming a livelihood for the economic activity of homo sapiens.

By the way, for those who didn't know, Venezuela -my country of origin- is one of the richest countries in the world in terms of biodiversity. For the international environmental organization VITALIS and other international organizations, Venezuela is among the TOP 10 countries in the world with the richest biological diversity. Not least considering that South America alone holds 40% of the planet's biodiversity quota: literally, a blessing of life. ^[1][2] Image 1 shows the countries with the greatest biological diversity on Earth (see image 1).

Indeed, 'biodiversity' implies concepts such as variety, multiplicity, abundance, among others that point to the idea of 'much/many': many individuals, many types, many characteristics, many populations, many distributions, in short, a lot of information. To develop all the subfields of ecology necessarily implies a substantial accumulation of knowledge which, in turn, necessarily requires an effective management of its registration and manipulation.

Furthermore, the availability of extensive information on biodiversity is the basis for much new scientific research and other projects. The compilation of data on species cases and their location can be used for phylogenetic reconstruction, forecasting the impact of climate change on the coming biodiversity, developing and verifying models on the suitability of the habitat, and even for estimating potential extinctions, their rhythms and consequent conversation initiatives; among many other reasons for research and applications. ^[3]

This is where the Global Biodiversity Information Faciliy, which stands for GBIF, appears. Its official website defines it as:

An international network and research infrastructure funded by the world’s governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth. ^[3]

In fact, this service is the largest international information system designed to facilitate access to vast data on the biodiversity of the entire planet. More than 1,433 institutions around the world have access to it and contribute by providing and sharing information freely, feeding the system, in addition to hundreds of other institutions and thousands of users who access it daily to obtain information.

That is why this platform is an example of 'open data management', since it makes specific data available to everyone in a completely free manner, without limitations by copyright and other forms of intellectual property that, on occasion, have proved to be detrimental to the progress of science. ^[4]

The genesis of GBIF is intimately linked to the interest of the countries belonging to the Organization for Economic Cooperation and Development in creating an "international mechanism" to achieve this mission of facilitating access to information on biodiversity, since it was determined that having a solid scientific basis within reach could save efforts in the growth of human knowledge about the natural world, in addition to contributing to improving the quality of life of society and - an argument that could not be absent - derive in "economic benefits". ^[5]

It should be noted that GBIF is also an example of the potential of databases for scientific research, an aspect suggested in a previous essay on preliminary database issues (in Spanish), in the sense that the platform provides and links different repositories with scientific information. The member organizations from different countries are grouped as 'nodes' and are the ones that provide the databases that are linked and cooperate in a single distributed system that contains species record, datasets, register of publishing institutions, among others.

To get an idea of the magnitude of data provided by this system, it is worth mentioning that at the time of writing these lines, I had a record of cases of 1,323,037,353 units, that is, more than a billion occurrences on the species known by GBIF! Regarding the number of registered species, the organization has clarified that it is difficult to provide an exact number due to different practical "complications" to interpret all the data, the names and distribution of the species. However, it estimates that there are 1,731,566 species reviewed included in its last Cataloge of Life and about another million "candidate species".

Technologically speaking, the system can be used through the official website , which offers a frontend quite comfortable for the consultation of information through the browser, supporting views in Spanish, French, English, Japanese and Portuguese, although most of the contents of the site are maintained in English. As an example, image 2 shows a query of the species Elaeis guineensis on the website (see image 2).

In the 'overview' you can see various data on the species, such as its complete taxonomy, a photographic gallery of specimens and a georeferencing through the rendering of a map highlighting the areas of the planet where the species is recorded, among other data. On the query, the site provides even more information of interest, such as the statistics shown in the 'metrics' section and links to datasets related to the species, all of which the secure user might find useful and intuitive to use.

Another of the service's technological resources is the Integrated Publishing Toolkit IPT, a free, open-source application that provides a standard graphical interface with which partner institutions feed the entire system. According to the GBIF website, the IPT currently has 266 installations distributed in 72 countries, including one installation at the Central University of Venezuela (UCV).

With this tool, a scientist at a GBIF-affiliated research center could compile 10,000 records of her arthropod research results into a spreadsheet and enter them into the IPT software. The latter will export all the information to a format called Darwin Core Archive (which we could talk about in a future post) and upload it to the GBIF network for further processing, which will end with the registration and publication of the information provided.

It should be noted that the use of this software requires some training and is logically indicated for those users registered and authorized to upload data to the GBIF, which is why I did not test the software in this post. In any case, a reference to an official tutorial on how to use the program is provided as follows.

So the GBIF has some key tools to be accessible to life science researchers, who have the quite practical website and the mentioned Integrated Publishing Toolkit (IPT), a client program to be used by affiliated organizations, such as universities, research institutes, etc.

But this is not all they have at their disposal! In a future article we will see that computer scientists and programmers who contribute to biodiversity research or develop computer applications can turn to the GBIF API to have 'repowered' access to the resources offered by the system. That will be entertaining to address.

In the meantime, biodiversity will still be the subject of much to be said, especially because of the threats it suffers as a result of human activities. The aspirations behind the founding of GBIF have been the pursuit of intellectual enrichment, social benefit, economic growth and sustainable development, and although the complexity of the problems and challenges facing life on planet Earth is very great, ecological science and technology can probably contribute to elucidating ways to make such aspirations a reality.

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REFERENCES AND RESOURCES USED

• [1] VITALIS (2014). Venezuela ranks ninth in the global biodiversity ranking. Article published in vitalis.net (in Spanish).
• [2] WorldAtlas (2018). The World's 17 Megadiverse Countries. Article published in worldatlas.com.
• [3] GBIF (n/f). What is GBIF. Official website document from GBIF.
• [4] Berge l, S. (2014). Scientific research and patents. Rev. bioét. (Print.). 2014; 22 (3): 416-.
• [5] GBIF (2010). Memorandum of Understanding for the Global Biodiversity Information System. Document consulted here.
• [6] GBIF Secretariat (2017). Introduction to publishing using the GBIF Integrated Publishing Toolkit (IPT). Tutorial available here (in English)

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EXPLANATORY NOTES

• Unless otherwise indicated, the images in this publication have been produced by the author, including the initial image, created with images in the public domain.