Jorrit Poelen edited this page Jul 9, 2017 · 16 revisions

introduction

The purpose of Effechecka is to create, save, export and follow checklists given specific spatial, taxonomic and trait constraints using data sources including, but not limited to, GBIF, iDigBio and EOL TraitBank. Example checklists include small birds and mammals of the San Francisco Bay Area and big sharks of the Gulf of Mexico. Matthew Collins of iDigBio presented a poster at TDWG 2015 in Nairobi, Kenia on the topic of whole dataset analysis and used Effechecka as an example.

Effechecka provides an api that can be used to re-create the prototype available through http://effechecka.org . This api is also used by https://gimmefreshdata.github.io . For more information, see https://github.com/gimmefreshdata/freshdata/wiki/api#checklist .

Currently, spatial, taxonomic and trait constraints are supported. In the future, we'll be adding the ability to save a checklist into an EOL collection. Also, we are working on a feature to help notify followers when a checklist (or the underlying data) change. Want to know more? Please open an issue or yell really loudly.

This project is supported by the Encyclopedia of Life and (partly) runs on iDigBio servers.

*A working prototype. Name is derived from "even checken," Dutch for "let's have a look."

spatial selector

The spatial selector specifies an area of interest. Currently, only a rectangular selection is supported for sake of simplicity, but underlying algorithms can use any arbitary WKT string.

taxon selector

The taxon selector specifies the taxa of interest. Scientific (i.e. latin) names can be added using the taxon lookup. The lookup lists taxa, including their higher order ranks, similar to the provided scientific or common name.

trait selector

The trait selector is used to select those taxa (e.g. species) that have a specific trait or traits.

syntax: [trait] [operator] [value] [(optional)unit]

Currently only bodyMass is a supported trait. Supported operators are: > (greaterThan), < (lessThan), =, and == (equals). Units g (i.e. grams) and kg (i.e. kilograms) are available. We expect to include more traits in 2015 - 2016.

Examples:

bodyMass > 50 kg
bodyMass < 11.2 g
bodyMass == 32 g

A trait selector "bodyMass > 2.7 kg" can be specified to include only taxa that have a body mass above 2.7 kilograms.

If no unit is specified (e.g. kg or g), the trait selector does a string comparison when the operator == (or equals) is used. So, if a source reports a value of "2.7" for the measurement body weight of the Black Vulture (Coragyps atratus) and the trait selector does not specify a unit, then "bodyMass == 2.7" will include the Black Vulture, but "bodyMass == 2.70" will not. However, when including the unit (e.g. "bodyMass == 2.70 kg"), the Black Vulture will be selected.

checklist

Checklists contain distinct taxa ordered by frequency of occurrence and are built directly from iDigBio's Darwin Core Archive (~15M specimen records) and an Global Biodiversity Information Facility (GBIF) archive (~450M occurrence records). Filters are available by taxonomic group and body size. On request, we can add more occurrence or trait datasources.

By clicking on "request checklist", the specified spatial, taxonomic and trait selectors are used to generate an ordered checklist of unique taxa: the most frequently occuring taxa with given constraints appear first. If the checklist has not been calculated before, the checklist generation may take several minutes. Please click the refresh button to check for results.

You can access your full checklist in several download formats, or if you have a user account on EOL, you can publish it there as a Collection. Currently capacity limits confine these to relatively small collections, so attempts at collections greater than 50 taxa may fail; we're working on this.

saving as eol collection

In addition to downloading a checklist as a csv or json file, you can save a checklist to an eol collection. This links the checklist items to taxon pages that are available on the Encyclopedia of Life. To save a checklist, Generate an EOL API key, specify how many items you'd like to limit the collection to, provide a title and description for the collection and click "save as EOL collection". For more detailed instructions, please see Save Checklist To EOL Collection.

If you find this feature too restrictive, you are encouraged to re-mix and re-use the functionality using the prototype source code at https://github.com/effechecka/effechecka.github.io and checklist data access api at https://github.com/gimmefreshdata/freshdata/wiki/api .

Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.