The MOL team is rapidly developing many features and new technologies. We are also rapidly increasing the number of species distribution datasets we make available. As we roll out new datasetss and features, you can follow our blog to learn what we are up to and provide valuable feedback and insight into the work we are doing.
Map of Life featured on Al Jazeera! (Note: Link not available within USA)
"Ever wondered which bird is making enough noise to wake you, or what strange creature scuttled under your bed while on holiday - a new free smartphone app is now available to answer those questions."
Several weeks ago we launched the Map of Life app for iOS and Android. It delivers a simple field-guide for tens of thousands of species worldwide to the palm of your hand and tailored to where you are. With an ever-growing coverage and functions it allows to instantly record species and potentially contribute important data for research and conservation. The app has been enthusiastically received around the world and seen some first reviews.
With over 25,000 downloads in the first eight weeks and already 500-1,000 regular daily users we are thrilled about the global uptake, rapid growth, and also the great feedback we are receiving. The app is available in six languages and we plan to add more in the near future.
Naturalists worldwide have already been using the power of the app to record and share their species observations. Over 1,300 different species from all major groups have been recorded in the first two months, with many sightings for undersampled places and species that dearly need more biodiversity information. We are currently working on a curation process before all data will be shared broadly.
App users can connect with their records in the app but also through an ever more powerful Dashboard on a dedicated web page.
An example personal dashboard:
Keep a list of species in your backyard or your regular walks, record the species seen on your trips, and develop a ‘life list’ of animals and plants seen. Learn more about how to record species here:
For more information about the app, see our Help page, which provides instructions and FAQs about the app. Check back with us as we grow the app, spread the word, and share any feedback via the within-app options or by emailing us, and - enjoy!
Map of Life has released a new species mapper. It provides all spatial data available for a species in the Map of Life, arranged by type and source, in a single interactive dashboard and map. Filter point observations by year and spatial uncertainty (large for old records with little documentation or surveys covering large areas, small for those new GPS contributions). Interrogate individual records and their sources by clicking on the map. Explore how different kinds of data tell different stories about species distributions. In the example of the Copper sunbird shown below, points, expert maps, and survey data all would result in very different assessments of the species’ range and environmental associations. Explore the map interface for this species, and check back as we add more facets, filters and tools to this map interface.
Nature reserves have a vital role for protecting biodiversity and its many functions. However, there is often insufficient information available to determine where to most effectively invest conservation efforts to prevent future extinctions, or which species may be left out of conservation actions entirely.
To help address these issues, Map of Life, in collaboration with Google Earth Engine, has now pre-released a new service to pinpoint at-risk species and where in the world that they occur. At the fingertips of regional naturalists, conservation groups, resource managers and global threat assessors, the tool has the potential to help identify and close key information gaps and highlight species of greatest concern.
Take the Tamaulipas Pygmy Owl, one of the smallest owls in the world that is restricted to highland forests in Mexico. The consensus range map for the species indicates a broad distribution of over 50,000 km2:
Left: Tamaulipas Pygmy Owl (Glaucidium sanchezi, photo credit: Adam Kent). Right: Map of Life consensus range map showing the potentially habitable range of this species.
But accounting for available habitat in the area using remotely sensed information presents a different picture: less than 10% of this range are forested and at the suitable elevation.
Users can change the habitat association settings and explore on-the-fly how this affects the distribution and map quality. This refined range map now allows a much improved evaluation of the owl’s potential protection. Furthermore, the sensitivity of conservation assessments to various assumptions can be directly explored in this tool.
The owl’s potential protection is likely to occur in only around 1,000 km2 that are under formal protection, representing seven reserves of which only two have greater than 100 km2 area. This is much less than would be desirable for a species with this small a global range.
Another species example, the Hildegard’s Tomb Bat, is similarly concerning: less than 6,000 km2 of suitable range remains for this forest specialist in East Africa, with less than half currently under protection.
A demonstration of this tool for 15 example species was pre-released at the decadal World Parks Congress in Sydney Australia last November to the global community of conservation scientists and practitioners. In the coming months this interactive evaluation will be expanded to thousands more species, providing a valuable resource to aid in global conservation efforts.
Read the article on Google Research Blog http://googleresearch.blogspot.com/2015/01/map-of-life-preview-of-how-to...
Use Map of Life to explore the evolutionary most distinct species at species.mol.org/info. For example, the Giant Ibis or the Oilbird.
Or use the species list tool map.mol.org/lists and search for birds to learn about how places differ in the distinctness of their assemblages.
Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, D. Redding, and A. O. Mooers. 2014. Distribution and conservation of global evolutionary distinctness in birds.Current Biology 24, 1–12, May 5, 2014 http://www.cell.com/current-biology/fulltext/S0960-9822(14)00270-X
The study quantifies evolutionary distinctness (ED), i.e. a species’ contribution to the total evolutionary history of its group, for all of the world’s 9,993 bird species and assesses which species are both distinct and rare (high EDR) or distinct and threatened (high EDGE). Species representing the most evolutionary history over the smallest area as well as some of the most imperiled distinct species are often concentrated outside the species-rich regions and countries, suggesting they may not be well captured by current conservation planning. The study demonstrates that with most species likely remaining ecologically understudied, combining growing phylogenetic and spatial data may be an efficient way to retain vital aspects of biodiversity.
Linking species values for evolutionary distinctenss (ED) and its rarity (EDR) to their geographic distribution supports identification of key potential priority areas for conserving phylogenetic diversity.
Potential priority areas for conservation for saving at least 60% of imperiled avian phylgenetic diversity following area selection by species evolutionary distinctness (ED, top 131 evolutionary distinct species). For details, see Figure 6 in study.
Potential top “conservation gap” cells for saving at least 60% of imperiled avian phylogenetic diversity. Cells in green flag the potential 113 top EDR “conservation gap” cells, red the additional cells ED based prioritization identifies, and orange further cells that only a “Random” (i.e. non-ED or –EDR focused) selection among Imperiled species would prioritize. For further details, see Figure 6 in study.
Map of Life lets you search by species name across the 366 million records we’ve imported so far. These records comes from fifty-four different datasets, some of which use different species names to refer to the same species. Last September, Rod Page pointed out one particular case:
The problem here is one of synonymy. A species may be referred to by a number of names over the course of its history: for example, the western hoolock gibbon, known today as Hoolock hoolock, was known asHylobates hoolock until at least the 1980s, when the name Bunopithecus hoolock was gradually adopted as the correct one. The species was then renamed Hoolock hoolock in 2005. (If you have access to an academic library, you can find all the details in Mootnick and Groves, 2005). Only one of these names is considered valid today; all the alternate names are known as synonyms.
Map of Life’s records come from a wide variety of sources, from century-old checklists to surveys carried out in the 1950s to expert range maps drawn in the 21th century. We have records for the western hoolock gibbon under all three names — Hoolock hoolock is used by the IUCN Red List, Bunopithecus hoolock by the WWF Ecoregion Species Checklists, and Hylobates hoolock by GBIF. This is a relatively simple case: the World Register of Marine Species (WoRMS) lists six alternate names for the Giant Pacific octopus. When you search for a name on Map of Life, the search results ought to contain not just the searched name but all alternate, synonymous names as well.
We decided that the best way to implement this would be by developing an in-house, expert-curated list of synonyms and accepted names, and to supplement these by using the new GBIF Species API. There are a wealth of options available today when picking web services for species name resolution, many of which make their entire list of synonyms available for download. We picked GBIF because of the large number of taxonomic checklists it incorporates — 270 separate checklists, including important taxonomic databases such as ITIS, WoRMS, the Catalogue of Life, Mammal Species of the World and others. These checklists cover every kingdom of life, giving us wide taxonomic and spatial coverage through a single JSONP query. It also allowed us to reuse our code for accessing this API from our work on name validation in OpenRefine.
When you search for a name on Map of Life, this is what happens:
Before anything else, we search for your query on Map of Life and present you with the results as quickly as possible, as we always have.
As you look through the direct search results, we search for your query in our internal list of synonyms. This table contains only vertebrate synonyms for now. If we find a match, we add the alternate names to your search.
If we do not find a match, we try to match your name against all of GBIF’s hundreds of checklists. If we find the queried name there, we add every valid name recognized for that species by any checklist to your search.
This turns out be a “good enough” solution for an incredible variety of names. Try searching for Caminus osculosus (a sponge), Octopus dofleini (an outdated name for the Giant Pacific Octopus), Anser hutchinsii (an outdated name for the Cackling Goose), or even the rotifer Lecane kasumiensis.
Synonymy on Map of Life isn’t completely solved yet: for example, we currently return only one of the two possible synonyms for Hoolock hoolock. This is because we currently look up only the valid name of the species you search for: a search for Hylobates hoolock will display records stored under its valid name,Hoolock hoolock, but will not display records stored under its alternate synonym, Bunopithecus hoolock. The next step is to look up not just the valid name, but all synonyms ever used to refer to that name, so that we can find every record which might be relevant to your search. This should be achievable using GBIF’s/species/search API call, as long as we make sure that these searches can be made fast and responsive, and don’t add too many unhelpful names to your search.
What do you think of our new feature? Please let us know if you have any problems with it, or have suggestions on how we can improve it!
of Life has grown significantly to include almost all taxa. This now takes us far beyond the focus on terrestrial vertebrates of the original Map of Life demo website launched almost a year. If you haven’t peaked at the Dashboard in a while, or searched on your favorite plant or invertebrate species, try it now! Whether its trees of North America, palms of the New World, or the beetles of Canada and Alaska, there is more to discover than ever before. Try out mappinglife.org/Socratea exorrhiza (the Walking Palm) to get a flavor. And check back for additional data sets in the future.
We have also made significant improvements to the user experience, and one highlight is the way you can now retrieve information about underlying biodiversity data sources right from the map. With a species mapped, set the “Identify Layers” option to “On”. You can now click anywhere on the map and get more information about which data sources support the occurrence of a species in the area. You’ll see a pop-up box with the different data types, and when you click on a data type, you can look at the individual records more fully, even getting links to the original sources.
We’ll be announcing a lot more new and exciting developments on Map of Life in the near future, so we hope you’ll check in often and give us continued feedback.
A quick Map of Life update as we head into the winter holidays. The big news is that you now have much more control over the look and feel of the maps via layer styling! Lets take a peek how that works. Select a taxon, say, something winter holidayish like this: http://www.mappinglife.org/Rangifer_tarandus. Or if you prefer to not be reminded about wintery cold, take a look at geographic information for the Eastern Yellow-Billed Hornbill (http://www.mappinglife.org/Tockus_flavirostris.
In the layers widget, you can style all to one color by selecting “style all” or you can individually edit the style of a layer by selecting the left-most icon, which is a symbol showing the layer “view”. For points, it default to a red dot, for others a solid fill color. When you click it, a layer styling pop-up box will appear where you can select a fill color, border, width and opacity. For range maps, where there are many colors representing different part of a species range, you can select each color separately. Take a look especially at the gridded survey for the Eastern Yellow-Billed Hornbill ,and try changing the color and add a one pixel border – its a nice way to really bring that kind of data forward on the map. Try it out, tell us what you think! We’ve been thinking about this one for a long time and so great to have it finally available for you to use!
More next year! Your Map of Life Team.
We are excited to announce a major upgrade to Map of Life! Lets walk through all the changes:
Map of Life is growing fast! We expect a lot more date to be made available soon and we very much hope you want to check it out again if you haven’t seen it in a while. Although the core remains the same, there are major additions and improvements across the board!
We have been so excited to see (and read about) all the interest in Map of Life since we launched our public beta in May 2012. Since launch, we’ve been quietly and industriously working on many new features and growing the data that Map of Life makes available. At the same time, we have been working hard to streamline and boost performance. A lot of this has been happening in the background, but we wanted to tell you a bit about a couple new features now live on the site and to also welcome some new folks to the team. To keep this short, you can learn all about new team members on our People page, but welcome Tom Auer (Yale), Peter Erb (CU Boulder) and Carsten Meyer (Georg-August-University of Göttingen).
Now onto the fun stuff. Our big news is that we have a much enhanced species list tool developed in the Jetz Lab. To try the new tool out, just go to our mapping tool, and right-click (or ctrl-click on Macs) on a spot on the globe, and you will get a list that includes tabs for images of species found at that spot, along with a chart showing percent of species at different levels of threat as defined by the IUCN (International Union for Conservation of Nature) Red List. You can also now download the list as a comma-delimited file. The other main feature is that now you auto-zoom to the broadest extent of layers when you hit “Map Selected Layers”.
More features and datasets are coming soon, so stay tuned! And please do send along feedback. Your suggestions and thoughts continue to inspire us.
This is a lits of press coverage for Map of Life in the last year. Please let us know about any typos, mistakes or broken links in this list!
It’s been an exciting month for Map of Life! We had a great time at TDWG 2011 in sunny New Orleans, where John Wieczorek and I presented Map of Life‘s big dream: to use existing maps to make better maps of where species actually are. John and Aaron Steele also presented some radical ideas about hooking CouchDB and CouchApp together to build simple, powerful applications. Their switch in strategy made us wonder if perhaps we could pull that off with Map of Life, too.
It was in this frame of mind that we attended Javier de la Torre's demonstration of CartoDB, a Google Fusion Table-like application to store and render mapping data. The more we saw, the more we liked: open-source (http://github.com/vizzuality/cartodb) (and available on GitHub!), based on PostGIS on PostgreSQL (already our platform of choice), and incorporating Mapnik, the super-fast tile rendering engine we discussed in our last blog post. They’re also quick to respond to our requests: last week, CartoDB added support for per-request tile styling, an essential feature for the next phase of our development.
Over the last two months, we’ve been working on moving our map tiling infrastructure to leverage CartoDB while continuing to use Google App Engine for indexing and searching. Although there are still some small glitches to work out before we can claim full success, our system now works in two parts:
A set of scripts which upload data into a CartoDB database, and; A frontend which queries and accesses that database to create a map to show our users. In so doing, we’ve reaped the rewards of a much smaller, simpler code base. Many of the more complicated tasks we were doing earlier, such as indexing our attributes or drawing the map layers, are now being handled by programs perfectly designed to take on these tasks (PostgreSQL and CartoDB respectively). So our job has been simplified to doing what we do best: managing the data, combining it easily and quickly in our front end, and analysing it for global patterns on our back end. We’ll be working to further simplify this upload process soon, and we’ll be showing off more of our new architecture shortly. Stay tuned!
Welcome back to the Map of Life blog! I’m Gaurav Vaidya, a first-year graduate student at the Guralnick lab in beautiful Boulder, Colorado. I joined the Map of Life team just under two months ago, and have been having a great time working on the project. In these two months, Map of Life has had a lot of fantastic new features approaching completion, and we thought the time was ripe to show some of them off to you!
Our most impressive new feature is our map rendering. As you may recall from earlier blog posts, mapping is handled by our backend, set up on a Linode VPS server. Aaron recently restructured our backend to useWindshaft, a high-speed map tiler generously released under an open-source license by Vizzuality, based on cutting-edge open-source tools such as Mapnik, PostGIS, Redis and node.js. Between Windshaft and Aaron’s work on HTML5 canvas, we’ve achieved some unbelievable results. At the moment, we’re rendering tiles without caching in the hundreds of milliseconds time-frame. This includes support for species occurrence data, protected areas, expert species range maps, ecoregions or any other geo-referenced vector or point data you care to throw at it. Aaron is currently working on merging these innovations into our main data preparation work flow.
Meanwhile, John has been busy adding raster environmental layers to Map of Life, probably with PostGIS’ upcoming raster support. Supporting raster layers is a first step towards linking all the species geographic distribution data already in Map of Life to local environmental variables such as climate, land cover and vegetation. This will also help us facilitate analyses on our platform, meeting one of the key goals for Map of Life. We’ll definitely be talking more about the planned analyses in future blog posts, so stay tuned!
Map of Life depends on data producers, compilers, and aggregators to add their data to the project, so it’s vitally important to ensure that they can do so quickly and easily. With a lot of help from the entire team, I am taking a first stab at this process. Before the TDWG 2011 Annual Conference (only a week away!), we hope to have all the scripts in place to provide an efficient pipeline from shape files and accompanying Map of Life-specific metadata to pretty, searchable layers on your favourite browser. So far, we’ve managed to compress most of the functionality we need into one easy-to-use program. This is a great area of Map of Life on which to have started, since it lets me connect with all the components of the software — from data preparation to map visualization — while also giving me a chance to work closely with the entire team.
There are many other exciting things we’d like to talk to you about, from analyses we have planned, to our TDWG demonstration next week, to the first release of a demo you can play around with yourself. For now, though, this brief glance will regrettably have to suffice. Please ask us any questions in the comments — it’s a huge help for us in gaging interest in features for the software, as well as for topics we need to cover in future blog posts. As always, Map of Life’s source code and open issues are available online, so please do contact us or contribute there if you have any specific concerns.
Map of Life has been chugging along for about 6 months now in its current configuration and now seems like as good a time as any to step back and consider how far we have come and what might be next. The team working on Map of Life is such an interesting one. Geographically we are spread out across the United States, from the East Coast (Yale University) to the Midwest (University of Kansas), Mountain West (University of Colorado) to the Pacific Coast (University of California, Berkeley). We are also diverse by country of origin (Australia, Germany, U.S.A.), academic training (computer science, ecology, evolution, informatics) and skill set (programming, systems engineerings, informatics, macroecology, systematics, etc). A gratifying part of the first six months, for me, is that these differences and diversity has translated into a strong working relationship and collaborative spirit, where the strengths of the group, not the weaknesses, have multiplied. I think this likely reflects a strong impetus to meet regularly, as often as three times a week, via cell or Skype, to synchronize efforts. Plus, good peeps and – turns out – we like working with each other!
So what have we accomplished with all this good will and great vibes? A lot, as it turns out! Much of that is “behind the scenes”. Andrew Hill and Aaron Steele have been bouncing great ideas back and forth about how to create an information architecture that is robust, scalable and efficient. We’ve put together a broad technological overview. As it stands now, and looking back, we have done a lot. First, we deployed a cloud-based copy of the Catalogue of Life, accumulated a large set of range maps for amphibians and mammals, checked taxonomy of those range maps against the Catalogue of Life database, and provided an initial mechanism to search those maps. Next we have developed the means to display range maps via Google Maps, using a map tiling tool named Mapnik, and developed some initial user interface frameworks and designs. We are currently polishing off access and display of species occurrence data points. All of this is great, but we are still treading in known waters. The excellent AmphibiaWeb project has also developed the means for displaying range maps and occurrence data points, for example.
Soon we will be pulling together some new types of distribution data such as “occurrence polygons” — places where species have been described via species list — and habitat preferences such as “wet broadleaf forests” or “shortgrass prairie”. These are new challenges for storage, query and visualization. An even greater challenge will be trying to provide all these sources of knowledge in a single search and user interface. Exciting times for Map of Life! We are looking forward to having some demonstrations soon, so you can try out some Map of Life features. Stay tuned (and thanks for reading).