The Map of Life

integrating species distribution knowledge

New feature: better synonymy in Map of Life

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:

An extract from Rod Page's blog post talking about a problem with how Map of Life treats names

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 as Hylobates 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:

  1. 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.

  2. 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.

  3. 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!

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Written by Gaurav

February 4, 2014 at 5:44 pm

Posted in technology, updates

Now over 500,000 species and over 350 million records in Map of Life, with new ways to discover

We are pleased to announce that Map 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.

Capture2

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.

Capture

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.

Your Yale and Colorado Map of Life Team

Written by walterjetz

April 30, 2013 at 7:50 am

Posted in Uncategorized

Stylin’! New user-controlled styles and more!

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.

Written by Rob

December 17, 2012 at 10:31 pm

Posted in Uncategorized

Building a better map (of life)

We are excited to announce a major upgrade to Map of Life! Lets walk through all the changes:

1) An upgrade to the user interface. You’ll immediately notice one useful feature — you can easily hide most of the widgets (e.g. the search widget, the layers widget) so that you can more easily explore the maps. You can just as easily show the widget again via open/close arrows. We have also moved elements around to be more sensible, so that the species list tool and species search tool are both at the top of the mapping application, and most of the other, ancillary map controls are at the bottom. The new design really optimizes screen real-estate for looking at maps, which is what we are all about.

2) The species list tool is much easier to use. You just need to click anywhere in the map when the tool is turned “on” and you get results. You can toggle the tool ON/OFF easily, in case you don’t want to have clicks generate list results.

3) You should definitely click on the “dashboard” for two reasons. First, the dashboard has been completely re-designed. Our initial dashboard was a blocky table of providers and sources. The new one is a much nicer list of datasets, explaining the source of those data, the type of dataset, and number of species names and records. The very top of the dashboard provides some summary statistics over all the datasets. You can easily filter a list by using the handy text boxes also near the top of the dashboard. If you enter, for example, “Loc” into the “type” textbox, you filter just to “Local Inventories”.

4) The second reason for clicking the dashboard is to see the 36 new datasets included in Map of Life. These new datasets include a new “type” of dataset, called a “gridded survey”. We have ten gridded survery datasets, mostly bird atlases from Africa. You can see how these gridded surveys display on Map of Life – as “cells” of different sizes representing presences from survey work. Search on an African bird taxon such as “olive sunbird” to check out these gridded products.

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!

Written by Rob

October 22, 2012 at 8:10 am

Posted in Uncategorized

New features in Map of Life

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”.

Image

More features and datasets are coming soon, so stay tuned!  And please do send along feedback.  Your suggestions and thoughts continue to inspire us.

Written by Rob

September 27, 2012 at 3:36 pm

Posted in Uncategorized

Press coverage of Map of Life

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!

Written by Gaurav

September 25, 2012 at 6:54 pm

Posted in overview

OneEarth, “GPS for Critters”, August 2012

This is not your grandmother’s blob map. The distribution data are nearly infinitely searchable and can be made almost instantly visible. A user can ask a basic question like “Where in the world is the yellow wattlebird?” and get an answer in unprecedented detail. One can map the whereabouts of dozens of species simultaneously, or pick a spot large or small, in Borneo, or British Columbia, or Chicago, and ask: “What are all the species that are found nearby?”

— Alan Burdick, GPS for Critters, OnEarth: August 30, 2012

Written by Gaurav

August 30, 2012 at 4:59 pm

Posted in Press