El mapa que explica la deforestación en el mundo (y lo hace en tiempo real)

Varios organismos lanzan Global Forest Watch, una web que integra capas de datos para ver el estado de los bosques de todo el mundo

Los mapas los pone Google; las imágenes de satélite, la NASA; los datos, el World Resources Institute y otras agencias; y la capa de visualización, la empresa española Vizzuality

El recurso sirve para gobiernos, empresas, comunidades y para que cualquier ciudadano explore los cambios forestales casi según suceden, porque los datos se actualizan con frecuencia

 Global Forest Watch.

Mira el mapa. El rosa representa la masa forestal que ha desaparecido en España desde el año 2000. ¿Qué pasa en Galicia, que se ha perdido tanta? "Muy fácil: en Galicia se producen el 50% de incendios de España", responde Ángel Dorrio, técnico de Medioambiente de la asociación Amigos da Terra.

Las estadísticas del Ministerio de Agricultura y el mapa de España en Llamas confirman que Galicia es la comunidad en la que más hay. "Como ves, siempre aparece Galicia en rojo. Los datos son graves, llevamos más de cuarenta años con el mismo problema". Un caso reciente es el de las Fragas do Eume. Si hacemos zum, vemos con detalle la zona devastada. La captura de la izquierda es el parque entre 2005 y 2009; la de la derecha, entre 2005 y 2013. En abril de 2012, el incendio extinguió más de 750 hectáreas (que son las que aparecen en rosa).

Ahora mira esta otra imagen:

Es una de las áreas del mundo en la que más árboles desaparecen. Aunque la del Amazonas es la más sonada, lo de arriba es el zum sobre la región de Gran Chaco, entre el sur de Brasil, Argentina y Paraguay. ¿Qué pasa? ¿Por qué la deforestación allí es cuadrada? Se llama sojización y es el cultivo de soja. "En Argentina y Brasil ha crecido brutalmente. Sustituyen cultivos tradicionales por monocultivo y hay mucha deforestación", explica Tom Kucharz, de Ecologistas en Acción.

¿Y por qué soja? Es más barata ("es agricultura intensiva con muchísima tecnología y fertilizantes químicos para matar la mala hierba"), sus proteínas son perfectas para la ganadería industrial (la que usan las cadenas de comida rápida, por ejemplo) y se vende muy bien en los mercados internacionales.

Este gráfico muestra la evolución de su precio, que sólo de 2007 a 2008 subió un 86%. Como Kucharz, ecologistas e investigadores llevan años alertando sobre el problema y sus efectos económicos y sociales. También sobre los medioambientales, claro.

Pintar los cambios de los bosques

Galicia y sus incendios, y el Gran Chaco y su sojización son sólo dos de los casos de deforestación que hay en el mundo. Las imágenes para explicarlos las hemos sacado de Global Forest Watch, un proyecto del World Resources Institute presentado la semana pasada que, en forma de web, muestra el estado de los bosques del mundo.

Los mapas los pone Google; los datos de árboles desaparecidos y aparecidos e imágenes de satélite, organismos como la Universidad de Maryland o la NASA. Y la visualización de esos datos (o cómo ver, en una imagen, que los incendios forestales en Galicia o los cultivos de soja se cargan los bosques), la empresa española Vizzuality y su tecnología CartoDB (que en eldiario.es hemos utilizado, por ejemplo, para ver el tráfico ferroviario en España).

"Lo que nos gusta es contar historias y los mapas son un medio para ello", explica Carlos Matallín, uno de los desarrolladores que ha ‘pintado’ las capas de datos. "Tenemos datos muy ricos, importantes y validados, pero que no puedes tirar en crudo porque no se saca nada en claro. Puedes decir ‘sí, hay deforestación’. La parte bonita, interesante y compleja es cómo muestro estos datos a cualquier persona de forma amigable e intuitiva. Y con ello, contar, por ejemplo, la deforestación en un área protegida y cómo a través de las alertas se puede parar". ¿Alertas?


Si un árbol cae y nadie lo escucha, ¿hace ruido?

Un problema de la deforestación es que cuando se detecta (cuando el árbol cae en mitad del bosque) suele ser tarde para pararla. Por eso la novedad de Global Forest Watch, que lleva dos años en desarrollo y del que ha habido prototipos previos, es el tiempo real: los datos que integra no sólo son de muy buena calidad (aquí explican de dónde proviene cada set de datos y cómo se ha tomado), sino que en muchos casos se actualizan diaria o mensualmente. También la posibilidad de delimitar áreas, guardarlas y poner alertas que te avisen si 'algo' cambia (si algún árbol cae en mitad del bosque).

.

"La página dice: 'near real time' (casi en tiempo real). La capa de fuegos, por ejemplo, se puede tener con hasta un día de diferencia. En cada capa están explicadas la resolución de los datos y la periodicidad con la que se actualizan", cuenta Matallín. Las capas más importantes son las de Forest Change (el cambio en los bosques, que dentro de la web está en la columna de la izquierda). "Queremos saber cómo está cambiando el bosque y eso viene explicado ahí. El resto de las capas (biodiversidad, masa forestal, zonas intactas o protegidas) ayudan al análisis".

Haciendo zoom, activando y desactivando capas de datos, puedes encontrar historias de deforestación o reforestación. Además de los incendios gallegos o sojización, en este post hay otros nueve ejemplos para entender lo que pasa en los bosques del mundo.

Rompiendo la barrera entre la ciencia y las personas

Más allá del ‘wow, qué mapa tan vistoso’, la herramienta es útil para muchos agentes. "Sirve para diferentes tipos de personas que quieran trabajar con los datos. Agencias gubernamentales, o no, que quieran controlar la deforestación, grupos indígenas que quieran saber qué está pasando con su tierra o empresas que quieren asegurarse de que su cadena de distribución cumple con los compromisos", precisa Matallín.

"Digamos Unilever o Nestlé, que son empresas que han dado su nombre. Nestlé tiene proveedores que están explotando un área. Ellos pueden ir a esa zona, hacer un análisis y confirmar que lo que les han dicho sus proveedores coincide con lo que ellos ven a través de la web".

Y más allá de gobiernos, empresas y grandes organizaciones, el objetivo de Global Forest Watch es llegar a la gente: con la posibilidad de enviar historias para explicar, con fotos, palabras y ejemplos, qué pasa en los bosques del mundo (¿hay un incendio en Valencia?, ¿en la isla de Sumatra? Envíaselo para que aparezca sobre el mapa) y que cualquier ciudadano lo explore.

"Con los datos en números no haces nada. Con esto acercas un poco más, o ayudas a romper la barrera que hay entre la ciencia y las personas. Que, al fin y al cabo, es lo importante y realmente crucial de este proyecto".

ORIGINAL: El Diario (España)

Analía Plaza
02/03/2014

The Genomic Standards Consortium

ORIGINAL: PLoS Biology

Dawn Field1*, Linda Amaral-Zettler2, Guy Cochrane3,James R. Cole4, Peter Dawyndt5, George M. Garrity6, Jack Gilbert7,8, Frank Oliver Glöckner9, Lynette Hirschman10,Ilene Karsch-Mizrachi11, Hans-Peter Klenk12, Rob Knight13,Renzo Kottmann9, Nikos Kyrpides14, Folker Meyer7,15,Inigo San Gil16, Susanna-Assunta Sansone17, Lynn M. Schriml18, Peter Sterk19, Tatiana Tatusova11, David W. Ussery20, Owen White18, John Wooley21

1. Centre for Ecology & Hydrology, Maclean Building, Crowmarsh Gifford, Wallingford, Oxfordshire, United Kingdom, 
2. The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 
3. European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, 
4. Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America, 
5. Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium, 
6. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America, 
7. Argonne National Laboratory, Argonne, Illinois, United States of America, 
8. Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America, 
9. Microbial Genomics Group, Max Planck Institute for Marine Microbiology and Jacobs University Bremen, Bremen, Germany, 
10. Information Technology Center, The MITRE Corporation, Bedford, Massachusetts, United States of America, 
11. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America, 
12. DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany, 
13. Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America, 
14. DOE Joint Genome Institute, Walnut Creek, California, United States of America, 
15. Computation Institute, University of Chicago, Chicago, Illinois, United States of America, 
16. LTER Network Office, Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America, 
17. University of Oxford, Oxford e-Research Centre, Oxford, United Kingdom, 
18. Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America, 
19. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, 
20. Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark, 
21. University of California San Diego, La Jolla, California, United States of America

Abstract

A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

Citation: Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, et al. (2011) The Genomic Standards Consortium. PLoS Biol 9(6): e1001088. doi:10.1371/journal.pbio.1001088

Published: June 21, 2011

Copyright: © 2011 Field et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: NERC International Opportunities Fund Award NE/3521773/1 and NE/E007325/1 (http://www.nerc.ac.uk/funding/) and National Science Foundation grant RCN4GSC, DBI-0840989 (http://www.nsf.gov/funding/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: GSC, Genomic Standards Consortium; MIxS, Minimum Information about any (x) Sequence

* E-mail: dfield@ceh.ac.uk

Introduction

We currently have thousands of genomes, hundreds of metagenomes, and tens of thousands of marker gene data sets in the public domain, and these numbers are rapidly increasing [1]. Next-generation sequencing technologies promise to further fill the public databases with a bounty of information unthinkable even a few years ago. Each data set represents an organism or community with a unique biological history, sampling location, environmental context, and set of biologically interesting traits. Hence, each of these data sets makes a unique contribution to the ongoing creation of our public online catalogue of life.

We are now witnessing the rapid democratization of access to sequencing capacity—an immense opportunity for the global community, if proper stewardship of these data keeps pace [2],[3]. This stewardship must include enriching public sequence databases with the biological context of these sequences (Box 1), which will in turn necessitate the adoption of a fresh attitude to reporting results, both in our papers and our submissions to the public databases. Large, well-contextualized genome, metagenome, and marker gene data sets (e.g., ribosomal gene surveys) provide ideal opportunities for comparison and contrasting using computational means to solve a wide range of questions in biology (including questions in medicine, physiology, developmental biology, biogeochemistry, evolution, ecology, etc.).

Box 1. When the Cost of a Bacterial Genome Sequence Is Almost Nothing, That Organism's Contextual Information Is Increasingly Valuable

Consider the scenario where a new E. coli sequence has been obtained from a futuristic handheld device (like a Star Trek tricorder) that generates the complete genome in seconds. While the genome sequence may only be slightly different from strains already in the public databases, the metadata associated with this bug is both unique and crucial. Where and when was the E. coliisolated? Was it transmitted as a food-borne pathogen? Did it hospitalize the patient from whom it was isolated? Was it part of a larger infectious outbreak? Knowledge that a pathogen was isolated from diseased patients or healthy controls will readily assist in intervention strategies derived from machine-readable data.

These data sets should be treated as part of a larger whole—a catalogue of life on earth—that will allow us to observe, as we sample in time and space, how life changes. A range of ongoing and proposed megasequencing projects also promise to make great inroads into this grand vision (i.e.,

• the Genomic Encyclopedia of Bacteria and Archaea [GEBA] [4], 
• Human Microbiome Project [HMP] [5], 
• Microbial Earth Project [http://genome.jgi-psf.org/programs/bacte​ria-archaea/MEP/index.jsf], 
• Earth Microbiome Project [6], 
• Genomes 10K [7], 
• Tara Oceans [http://oceans.taraexpeditions.org/], 
• Malaspina [http://en.wikipedia.org/wiki/Malaspina_E​xpedition_2010],
• Sorcerer II Global Ocean Sampling expedition [8]).

How must we now change the way we think about these data sets to prepare to integrate and co-analyze these large suites of related and contrasting data? Clearly, these data must be stored in robust comprehensive electronic systems that link to specific environments, diseases, or physiological states such that these relationships are electronically retrievable. To achieve this goal we urgently need shared standards that are both easy to use and scientifically robust.

The Genomic Standards Consortium

The GSC was established in late 2005 [9],[10] to tackle the challenge of working towards better descriptions of genomes and metagenomes through community-level, consensus-driven solutions. The GSC's mission is to work towards 1) the implementation of new genomic standards, 2) methods of capturing and exchanging the information captured in these standards (metadata, or contextual data) and 3) harmonization of information collection and analysis efforts across the wider genomics community.

The GSC fulfils this mission by holding face-to-face meetings, forming working groups, and building consensus products that can be widely used in this community. Thus far, the GSC has created a standard, the Minimum Information about any (x) Sequence (MIxS), that includes three minimum information checklists for describing genomes, metagenomes, and environmental marker sequences (MIGS/MIMS/MIMARKS) upon submission to the public databases and publication [11],[12]. MIxS requires core information on habitat, geolocation, and sequencing methodology as well as fields specific to data type and a range of optional environmental packages to capture core measurements defining a broad range of habitats, including water, soil, and host-associated habitats. The International Nucleotide Sequence Database Collaboration (INSDC; DDBJ/EMBL/GenBank) has created a GSC “keyword” (MIxS) to mark the richer entries complying with this standard.

Other working groups are dedicated to

1. the maintenance of an extensible markup language (GCDML) that provides a reference implementation of the MIxS checklists [13], 
2. development of tools and software, 
3. compliance and curation, and 
4. biodiversity. 

Those requiring help complying with MIxS (curation support) should contact the compliance working group, and those requiring technical assistance in implementing/adopting these standards in software or database projects should contact the developer's working group (technical support). The developer and compliance groups work closely together, for example, to support compliance through a range of portals, including GOLD [1], MG-Rast[14], CAMERA [15], IMG/m [16], the RDP [17], SILVA [18], megx.net [19], and the ISA software suite[20]. The Biodiversity group works with communities to make sure that GSC standards evolve in harmony with standards for describing taxonomy and biodiversity.

The GSC has also stepped forward to create a journal designed to underpin the emerging field of standards development in the biological sciences [21]. The Standards in Genomic Sciences journal now serves as a formal voice for the GSC and supports the publication of standardized genome, metagenome, and pan-genome reports and other standards-supportive publications like Standard Operating Procedures (SOPs) [22] from the scientific community at large.

The GSC is now maturing into a hub for the coordination of large-scale projects. Two projects running under the GSC umbrella are the Microbial Earth Project, which calls for the coordinated sequencing of over 9,000 type strains (http://genome.jgi-psf.org/programs/bacte​ria-archaea/MEP/index.jsf), and the M5 project, which calls for the coordinated development of a next-generation computational infrastructure (http://gensc.org/gc_wiki/index.php/M5) [23].

The GSC also works closely with a range of related communities and helped drive the formation of the Environment Ontology [24], the Minimum Information for Biological and Biomedical Investigations (MIBBI) initiative [2], and most recently the BioSharing forum [3, 25].

A Call for Participation and Adoption

The Internet has resulted in a Cambrian explosion of productivity and data sharing through the adoption of a huge stack of agreed-upon protocols (standards) that allow many devices and programs to communicate to the transformative benefit of the everyday user [26]. Enabling access to user-generated content is key to harnessing the resources of a distributed community: Flickr has over 5 billion photographs uploaded, and Wikipedia has over 3.5 million English articles as of this writing. Standards for organizing sequence data will be similarly needed as sequencing instruments themselves, especially as these instruments are more and more commoditized and owned by individuals rather than institutions.

The tagline of the GSC is “Innovation through Collaboration”. For any standard to create a lasting impact requires substantial input from the wider scientific community, including adoption and support. The GSC urges researchers interested in pushing the boundaries of genomic science through collaboration to join and contribute expertise to building the GSC roadmap for the future. Membership in the GSC and all working groups is currently defined by participation. The GSC has a Board and several standing committees in addition to its working groups. For more information on the GSC, please see http://gensc.org/.

Conclusions

The GSC is working to become the authoritative working body in the area of genomics for the development and adoption of standards. We anticipate that the need for a collaborative body in which to build consensus at the community level and undertake large-scale projects will only increase with time, as in many ways the era of genomics is just beginning. In the future, sequence generation will only increase as access is further democratized. On one extreme, it will be like any other industrial commodity and will be outsourced into a global manufacturing marketplace. On the other, mid- to large-scale sequencing will be as locally accessible as a benchtop microscope or PCR machine is to a typical university researcher. Making these diverse streams of data accessible in a coherent framework will require new, standardized ways of describing, storing, and exchanging this information. The framework required to do this will involve acceptance of profound sociological and technological changes in how we do business in the genomic sciences.

Acknowledgments

The GSC acknowledges all participants in past GSC meetings for their thoughtful contributions. The GSC also acknowledges a range of funding sources for its past meetings, including NERC, NIEeS, NSF, the Gordon and Betty Moore Foundation and DOE. In particular, funding from NERC helped launch the GSC and allow essential infrastructure to be built. Funding from the NSF in the form of the Research Co-ordination Network (RCN4GSC) is supporting exchange visits of early career scientists and working group activities.

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Feria Mundial de las Ciencias de Google 2012

ORIGINAL: Google Science Fair

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La Feria de las Ciencias de Google es un concurso de ciencias online que busca mentes inquietas de todos los rincones del planeta. Puede participar cualquier persona interesada que tenga entre 13 y 18 años de edad. Solo tienes que tener una idea.

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