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Equus burchellii (Gray, 1824)
Plains zebra


Updated: 1 October, 2014


Timemachine

Overview

Here, we tell about our Timemachine, discuss the natural history collections it contains, and explain how to use its interface.

Understanding labels

Specimen records in the Timemachine have two main parts. In our digital pohtographs you will find 1) a museum specimen (e.g. an insect or plant) and 2) the labels that go with it. We need your help to capture information from these labels.

Collection label
   Where: country(assumed)= United States state= New Hampshire locality= Enfield
   When: date(yyyy-mm-dd)= 1973-08-03 or (literal) 3 AUG 1973
   Who: collector= R. Gray
Ownership label
   Ownership: The specimen is a part of the Dartmouth College Collection.
Determination label
   What: Hypoprepia fucosa was described in 1831 by Franz Hübner,
             abbreiviated here as Hbn.
   Determined by: The specimen was identified by A. E. Brower in 1973.
Unique identifier label
   Unique ID: YPM_ENT789639 uniquely identifies this specimen from all others.
   Database: The Entomology Division, Peabody Museum assigned this identifier.

Steps

  1. Enter the Timemachine

    Visit www.discoverlife.org/timemachine, or from the Discover Life homepage, type "timemachine" into the search box. On the Timemachine page, click "Get going."
    Get going.

  2. Tell us who you are
  3. We're keeping track of your time travel. Give your full name and a valid email address in the top two fields, so that we can tally your work and give you credit. Login with the same information each time you use the Timemachine. We will not make your email publicly available, but may use it to contact you.

  4. Transcribe the record

    Specimen records in the Timemachine have two main parts. In our digital photographs, you will find 1) a museum specimen (e.g. an insect or plant) and 2) the labels that go with it. We're interested in the collection label. The collection label tells the story of how each specimen was found and gives information like who, what, when, and where. For plant specimens, this label is most often in the lower right-hand corner of the photograph. For insects, it's usually the top label.

    Locate the collection label and transcribe into the form as much of the following information as you can, exactly as it appears in the photograph.

    If you don't see any information in the photograph for collector, date, or elevation, enter 'no collector', 'no date', or 'no elevation' for these fields, respectively.

    If you can't read the information but think that it's there, enter 'too hard'.

    If you are fairly sure but not certain, enter a comma and then maybe after your best guess, for example, 'Wm. Smuth, maybe'

    Our software does not yet support symbols, accents, double quotation marks, and parentheses. Please do not enter them.

  5. Click "submit".

    If you click submit without telling us who you are, your record will not be submitted. After a successful submission, you will be invited to select another record of the same kind or a random image.

Discover Life | Albums | IDnature guides | Global mapper | Search | Top

Albums

Setting upUploadingEditing

Overview

Digital photography offers a rapid and accurate means to collect vast quantities of information on species and their interactions. It is also an excellent way to engage students, teachers and others in science, empowering them to collect and share information in original research projects. Discover Life is working to better understand and manage the impacts of climate, invasive species, pollution and other factors in agricultural and natural systems by photographing species across our network of sites and by building custom on-line guides to help contributors identify their local species correctly. In this effort, we invite you to join us. For more details, please see Macrosystems Research.

Our albums enable contributors to upload and manage large numbers of images to document observations about nature accurately and quickly. One can upload hundreds of images at a time and then rapidly edit information about them, such as where they were taken and the names of species within them. While albums are password protected, taxonomic experts can collectively help contributors identify what is in their photographs.

As contributors add species, the system build each a personal life list that documents all the species that each contributor has photographed. Users can search and compare life lists by geographic location and date. With the exception of protected species, we map photographs that have geographic information. Thus, users can map where contributors have taken photographs and found particular species.

Setting up an album

  • Contact us
    Request an album by sending us with your name, email address, and other contact information. We will set up an album for you with a unique identifier, such as I_ABC, then send you a password and instructions.

  • Install Software
    Once you have an album, you then need to install software that will enable you to upload images in bulk. Depending on your computer, click on one of the following links that explains how to do this.

Uploading images to an album

You can upload images in bulk or individually.

Editing species names, location, and other information in an album

How-to Video -- Editing album information for where and when

The list of albums is alphabetical by last name. General users should click on a contributor's name to view an album. The [edit] links to the right of each name can be used by contributors, taxonomic experts, and general users as follows:

  • Contributors can edit anything in their album by clicking on the [edit] link next to their name. They can upload and remove images.
  • Taxonomic experts can edit the title and a few other fields in any album. However, they cannot edit other fields and cannot upload or remove images.
  • General users may use [edit] to enter an album and then use Find to search for images as described below. However, without a password, they may not make any changes to an album. A small proportion of albums are secure and require a password to enter [edit]. General users cannot search these.

Once in edit mode, you will enter a form that features the following from left to right

The following explains how to use the form:

Section under development

  • Log in section
  • Features and controls In blue, center two columns are Fields to enter information with labels for each to the right Template section -- defaults to previous image
    • Editing species names and other information
      • Your own album
      • Others' albums
      • Using IDnature guides to identify species
      • Scientific names

Discover Life | Albums | IDnature guides | Global mapper | Search | Top
IDnature guides

New users

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How to begin

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How to identify things

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Banner controls

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Building guides & checklists

Building guides and checklists is a two step process that involves (1) putting information into eXtended markup language (XML) files and then (2) making database (db) files from the XML files. The XML files are text based and can be read and easily manipulated by humans, either with a text editor or with a set of Web-based building tools. The db files are used by the 20q software to run the guides quickly. They can't be read by text editors and are built with the "refresh" tool (see "Building tools" below).

Security
To use the building tools, first select a guide and then click on "Menu" in the top banner. The building tools are displayed on the left. Everyone can use these tools to manipulate the XML files on the outside of a firewall. However, only authorized users can make permanent changes to the XML files through a process that involves email transactions or authorized IP addresses. If email is used, the tools store changes on the outside of a firewall and send an email with a PIN number to a specified email account. Permanent changes occur when the email with the PIN number is returned to the server and is authenticated against two files, one containing authorized email and IP addresses (20q_ALLOW) and the other, the transaction PIN numbers (20q_MAIL_PIN). The system ignores emails that are from accounts that are not authorized to change a specific guide or that contain a PIN number that is incorrect. Guide builders who reply to an email must include the original text with the PIN number in their reply or it will be ignored. Making changes is easier if the guide builder is working at authorized IP addresses. They simply use the tools and then "refresh" to make the changes permanent.

Step 1: On Pick18 (original), go to your guide of choice
Step 2: Update the end of the url like this -- guide=Moth&email=youremail@blank.com
Step 3: Hit 'controls' and then enter
Step 4: You will receive an email with a pin
Step 5: Re-update the end of your guide url like this -- guide=Moth&email=youremail@blank.com&pin=1234

Guides versus checklists
A guide and its associated checklist share a single XML file and are built with the same tools. However, they differ in which kinds of organisms they display. We define a kind as a unique combination of an organism's name, morph, and sex. To appear in a guide a kind must have at least one character-state. Kinds without any character-state attribute appear only in the checklist. Guides distinguish between morphs and sexes. Checklists do not, listing only kinds with different names. The order in which kinds are displayed in checklists has several options, is in flux, and is currently not documented. Generally, kinds are listed alphabetically by scientific name; however, in some cases, kinds may be listed in groups based on their "path," a variable that is set with the "score" tool (see "Building tools" below), that generally reflect groups such as orders and families.

If you are an expert in a group and wish to build a guide or help with one, please contact John Pickering.

Process -- one of elimination
Guide users and builders may have to switch their thinking to work with IDnature guides. Most other identification keys use a process of selection. In contrast, IDnature guides work by elimination. This difference gives IDnature guides a fundamental advantage in the practical world where some questions can't be answered. Antennae banded? Oops. They've been knocked off.

How to deal with unknown or unscored characters?

Building tools
Before reading this next section, please familiarize yourself with
20q XML Tags & File Structure.

The following tools appear on the left under "Menu." To use a specific tool, click on the box to its left and then on the "submit" button above it. Follow the instructions that appear in red after you select a tool.

Character & state conventions for choosing, naming, and presenting characters
Choosing, naming, and presenting the appropriate characters and their states is the hardest part of building a guide. Our goal is to use characters and states that the average 4th grade student can understand and recognize. While in some cases it may be impossible to avoid technical terms, please try. Also please try to avoid characters that require special equipment and methods that may not be generally available outside of research instiututions. For the most part we hope that binoculars, a hand lense, or a school microscope will be sufficent to successfully use the guides.

In choosing characters and states, there are several considerations that stem from the advantages and limitations of computer based identification. These are

Templates
To help you build guides, share character-states with other guide builders, and score kinds rapidly, IDnature guides use the following:

Further information
For further details on why and how to build guides and checklists, see

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Setting up a new guide

  1. In 20q, bak and vi 20q_ALLOW. Add the new guide name and the email of the person with authority to edit the new guide.
    • NOTE: add sam droege as authority to every bee guide.

  2. In 20q, bak and vi 20q_IMAGES. Add the new guide name and the path to the guide species.

  3. In 20q, bak and vi 20q_GUIDES. Add a link to the new guide in the "Others in development" section.
    • NOTE: bee guides are listed here: /home/web/dl/nh/tx/Insecta/Hymenoptera/Apoidea/index.txt.

  4. In 20q, cp TEMPLATE.xml to New_Guide.xml. Edit New_Guide.xml.

  5. On pick14 browser, go to guide=New_Guide. Error message will appear. Click 'Menu'; 'Refresh'. Credits should appear.

  6. Begin entering and scoring species!

For splitting existing guides:

  1. Follow above instructions, using one existing guide as template
  2. Go to /home/db/20q and delete old guide. Then scp new guides to www.
  3. Delete old guide .html here: /home/web/dl/nh/id/tmp/20q/html
  4. On www, go to /home/db/20q and chmod 664, chgrp nobody, chown nobody (be root for this one)

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Adding images -- type, resolution, and file name
This section refers to the older JP80000 image system.
The newer EL_DP and I_ will be documented elsewhere.

20q uses <image> tags to link images on the Web into the guides. While any image URL could theoretically be used to illustrate the guides, Discover Life and IDnature guides function better if guide builders follow the following conventions:

For further instructions on putting images on Discover Life and in IDnature guides, please see

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Overview

Discover Life provides web services to share its tools and content through other sites. Without seeking permission, any non-commercial website may customize links and forms in their pages to use the services described below. Commercial sites should not use them unless they have permission.

Here we explain how to write HTML <a href...> tags (GET queries) and web forms <form...> (POST queries) to pull up Discover Life's images and other content from within your site. You can customize these queries so that Discover Life generates navigation bars that link back to your pages. Thus, your users can easily return to your pages after viewing Discover Life content.

The basic principle is simple. You will use HTML to pass variables to Discover Life's servers that will then generate pages from our network of contributing databases. Each query will call a server and tell it what to do based on the variables you send.


Selecting a Discover Life server

You can call a Discover Life server dynamically or select a specific one. The link in the example above calls
      http://www.discoverlife.org/20/q?
which selects a server dynamically. Alternatively, you can call a specific server, such as
      http://stri.discoverlife.org/mp/20q?
Generally we recommend the first method. It allows Discover Life to load balance across its servers. Eventually, as our regional centers come on-line, we intend for you to be able to call servers by region and by language.


Customizing navigation bars

Set &btxt, &burl, and &bi variables to customize navigation bars. These variables let you present information within your site's framework so that it is not obvious to your end-users that Discover Life is working behind-the-scene. Customized navigation bars return users to your site after they have viewed material from Discover Life. While we credit photograhers and other content providers, you can in effect hide Discover Life's role to end-users. We do this to encourage other sites to share our content widely.

For partner sites that contribute information to Discover Life, we use a single variable, &b, that customizes our navigation bars and icons to match the look-and-feel of our partner's site. Please contact John Pickering if you wish us to set up this custom feature.

The following uses &btxt and &burl to link http://www.your.org/page.html to Your Organization in the tree guide's banner:
<a href="http://www.discoverlife.org/20/q?guide=Trees&btxt=Your+Organization&burl=www.your.org/page.html" target="_top">
Tree and vine guide</a>

  • &btxt
    • No spaces
      Do not put spaces in &btxt. Use plus signs instead.
      Thus, it's Your+Organization not Your Organization.

  • &burl
    • http://
      It is unnecessary to put http:// in &burl. It is the default.
      Thus, www.your.org/page.html and http://www.your.org/page.html are equivalent.

    • Linking to cgi scripts
      To link to a page generated by a cgi script, change the ?, &, =, and + characters as follows in the &burl variable:
             ? to :;q:; (i. e., colon semicolon q colon semicolon)
             & to :;a:; (i. e., colon semicolon a colon semicolon)
             = to :;e:; (i. e., colon semicolon e colon semicolon)
             + to :;p:; (i. e., colon semicolon p colon semicolon)

      For example, the HTML source code (without spaces or new line before &burl and &btxt)
      <a href="http://www.discoverlife.org/20/q?search=Abelia+chinensis
      &burl=
      taibnet.sinica.edu.tw/chinese/taibnet_species_detail.asp:;q:;gen:;e:;Abelia:;a:;spe:;e:;chinensis
      &btxt=TaiBIF "> <img src="http://www.discoverlife.org/favicon.jpg" border=0>Abelia chinensis</a>
      yields

             Abelia chinensis

      This uses Discover Life's search variable to generate a species page with navigation bars that link to a page generated from the TaiGIF database at Academia Sinica, Taiwan. After parsing the &burl value
             taibnet.sinica.edu.tw/chinese/taibnet_species_detail.asp:;q:;gen:;e:;Abelia:;a:;spe:;e:;chinensis
      it becomes
             http://taibnet.sinica.edu.tw/chinese/taibnet_species_detail.asp?gen=Abelia&spe=chinensis

    • is Discover Life's 16 x 16 pixel icon.
      Above we used <img src="http://www.discoverlife.org/favicon.jpg" border=0> to include this image.
      You may download and use this image from http://www.discoverlife.org/favicon.jpg.

  • &bi
    This variable lets you put your icon in the IDnature guide banner. Thus,
    <a href="http://www.discoverlife.org/20/q?guide=Trees&bi=www.your.org/your.jpg" target="_top">
    substitutes the image specified by http://www.your.org/your.jpg for the banner's default butterfly.
    • http://
      It is unnecessary to put http:// in &bi. It is the default.
      Thus, www.your.org/your.jpg and http://www.your.org/your.jpg are equivalent.

    • Icon size
      You may specify an icon of any size. However, we recommend one of 69 pixels high to match the height of the water lily on the banner's left, which is 80 pixels wide and 69 high.

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Put IDnature guides on your Web pages

Non-commercial sites are welcome to put links to IDnature guides on their pages. Other sites must have permission before doing so.

Before reading this section, please familiarize yourself with the overview and examples of how to use Discover Life's web services (see Web services overview).

  • Link to all guides
    <a href="http://www.discoverlife.org/20/q" target="_top"> IDnature guides</a>

  • Link to a specific guide
    <a href="http://www.discoverlife.org/20/q?guide=Trees" target="_top"> North American trees and vines</a>

    This uses ?guide= to specify a specific guide, i. e., Trees.

    • List of guides
      Please see guides and checklists for all available guides.

    • Case sensitive
      Note the guide name are case sensitive. You must call them as they appear in the master list. Thus, use Trees, not trees or TREES.

    • Underscores not spaces
      Guide names sometimes include underscores. They never include spaces. Thus use Insect_orders, not Insect orders.

  • Setting more variables
    You can set more than one variable, as in the following example:
          <a href="http://www.discoverlife.org/20/q?guide=Ants&show_images=off" target="_top">
    • Use question mark, then ampersand(s)
      The first variable always follows a question mark, thus, ?guide=. The second and any additional variables follow an ampersand, e. g., &show_images=. Thus, here we set ?guide=Ants and &show_images=off. This second variable speeds guide transmission by using links rather than displaying thumbnails automatically.

  • Default values
    It is not necessary to specify default values. In this above example, &show_images=on is the default. Thus,
          <a href="http://www.discoverlife.org/20/q?guide=Ants" target="_top">
    and
          <a href="http://www.discoverlife.org/20/q?guide=Ants&show_images=on" target="_top">
    are equivalent.

  • &flags
    Put the following options in the URL to change the way an IDnature guide works:
    For example,
    <a href="http://www.discoverlife.org/20/q?guide=EcoLibrary&flags=HAS:index_no:not_no:" target="_top">EcoLibrary</a>
    presents the EcoLibrary guide with three of these options turned on. Note that each option must end in a colon, even if there is only one.

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Linking to Discover Life's images and slide shows from your Web pages

Discover Life is assembling a collection of high-resolution images from our contributors that we encourage you to link to from other websites (see "Copyright and terms of use" below). We process and store our images at five resolutions, assigning each image a unique identifier. Here we explain how to call individual images, sets of images, make slide shows, view metadata associated with images, and change resolution. We assume that you are familiar with the overview and examples of using Discover Life's web services. If not, please goto Web services before continuing.


© Copyright Smithsonian Tropical Research Institute, 2003-2006


EXAMPLE IMAGE

Discover Life's images each have a unique identifier that you can use to link them into your web pages. For example, the image on the left has the identifier I_SP1284.

If an image has an identifier, use the following command to display it on your web page:
<img src="http://www.discoverlife.org/mp/20p?img=I_SP1284">
where the green part is the identifier of a specific images.

You can change the resoultion of most images by adding &res= to the url, for example:
<img src="http://www.discoverlife.org/mp/20p?img=I_SP1284&res=640">
increases the size to 640 pixels across. Resolution options are 80, 240, 320 (default), 640, and mx (maximum).

Please credit images with the text shown below the image when you call it with our &see= flag. For example, in this case,
<img src="http://www.discoverlife.org/mp/20p?see=I_SP1284">
specifies "© Copyright Smithsonian Tropical Research Institute, 2003-2006". It also usually specifies additional data about the image that you may display.


  • Copyright and terms of use
    Non-commercial sites are welcome to link to these images without seeking permission, so long as they (1) display any copyright text and links associated with each image and (2) respect the copyright and terms of use as specified by the contributor(s). Commercial sites must have permission from Discover Life or an image's contributor before using an image. Our contributors retain copyright and all legal rights to the use of their images.

  • On-site versus off-site images
    Discover Life's species pages present both on-site images, those that are store in our image center, and off-site images, those that we request on the fly from other sites such as CalPhotos. The following discussion only applies to on-site contributors, such as those listed under photographers, that are assigned an agent name and identifier.

  • Agents and their database identifiers
    Agents are individuals, organizations, and institutions that contribute images and other data to Discover Life. We assign each agent database a unique identifier, such as I_SP, which identifies Steve Paton's image database of Panamanian plant images.

    • Database identifiers
      Image database identifiers start with I_. Other databases, such as those containing specimen records for mapping, start with other combinations of capital letters.

    • Case sensitive
      Database identifiers contain only the capital letters A-Z and the underscore '_' character.

  • Unique image identifiers
    • Original images
      Each original image within an agent's image database is assigned a unique numeric identifier. For orginal images, these identifiers can have up to 6 digits, each ranging from 0 to 9. Thus, I_SP1284, is image 1284 in the I_SP database.

    • Crops from original images
      If an image is a crop or version of an original, it is uniquely identified by appending an underscore followed by a unique integer to its orginal image's unique identifier. Thus, I_SP1284_1 and I_SP1284_35 would be versions derived from the original I_SP1284 image.

  • Displaying an image and its metadata
    Using the following to display this image and its metadata at the default resolution:

          <a href="http://www.discoverlife.org/20/q?see=I_SP1284">
          <img src="http://www.discoverlife.org/favicon.jpg" border=0> Erythrina costaricensis</a>

    yields

           Erythrina costaricensis

    In short, use ?see= followed by an image's unique identifier, in this case I_SP1284, to display the image and its metadata.

  • Multiple images
    To display multiple images together, list their unique identifiers separated by semicolons (no spaces). Thus, I_SP1284;I_GA1643 is Steve Paton's plant image followed by ant contributed by Gary Alpert.

  • Resolutions
    Images are stored at five resolutions ranging from the original maximum resolution (mx) to a thumbnail that is 80 pixels along its largest side. The other resolutions are 240, 320, and 640 pixels in their largest dimension.

    You may change the resolution and display mode of images by setting &res= as follows:

    • &res=80 Displays thumbnails and their titles. Metadata is not shown unless a user clicks on a thumbnail.

    • &res=240 Displays 240 pixel images with their metadata.

    • &res=320 The default. Displays 320 pixel images and metadata.

    • &res=640 Displays 640 pixel images and metadata.

    • &res=mx Displays images at maximum size with their metadata.

    • &res=md Switches from the default of displaying multiple images in the same page to presenting them as a slide show.

  • Use the following option in the URL to change the way images are displayed:
    • &flags=index_no: -- drops navigation of directories at top of page but leaves it at the bottom.
    For example,
    <a href="http://www.discoverlife.org/mp/20q?res=240&see=I_JP/1622&flags=index_no:">images in I_JP/1622</a>

  • Use the following options with checklists:
    • &flags=build_html: -- rebuilds a cached checklist (20p) -- cannot be used with 'want' and 'wrap' below.
    • &flags=want\d+: -- format checklist (20p) -- where \d+ is an integer that controls number of images per kind.
    • &flags=wrap\d+: -- format checklist (20p) -- where \d+ is an integer that controls row wrap.

  • Displaying an agent/photograph's directory of thumbnails
    For each agent database, we store photographs in subdirectories that contain up to 100 original images, not including any images made from originals and identified by the original's identifier followed by an underscore and integer.

    The first directory is 0000; the second, 0001; the third, 0002, and so forth. You can display all the thumbnails in a directory with see=, the agent's unique identifier, a forward slash, and the directory number. Thus

    If one does not specify a directory, the first one containing an images is displayed as the default.

  • Examples
    You can combine the above variables:
  • Grading images
    We give images integers as grades. Zero is the default for ungraded images. Negative grades switch images off so that they do not appear in species pages. Higher grades will appear before lower ones on the species pages. Thus, 3 is a better grade than 2, for example.

  • Display crops from an original
    We number crops from an original with the original's unique identifier followed by an underscore and a unique integer. For example, the Equus burchellii image I_JP2119_1 used above was cropped from I_JP2119

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Global Mapper
The Global Mapper was developed through a technical partnership between The Polistes Corporation and Topozone.com. Topozone provided base maps and aerial photographs from servers in Massachusetts using a total of approximately 20 terabytes of data. These include 1:1,000,000 scale maps of the world, 17 million topographical maps to 1:25,000 scale of the United States, and aerial photographs at 1 meter resolution covering 89% of the United States. Using Discover Life's servers, Polistes integrates distributional data onto these from participating databases, such as Missouri Botanical Garden's. In 2003, Sun Microsystems, Inc., gave The Polistes Foundation a generous equipment grant that included 10 processors to help Discover Life expand its network and serve its users from the University of Georgia and Missouri Botanical Garden, in North America, and the Agricultural Research Council, in Southern Africa. We seek additional partners to add more maps, photographs, databases, and regional servers to Discover Life.

Functions

  • Help - Shows this help.
  • Find place - A map will appear after you fill in the form and click on submit.
  • Make custom map - Build a map of anywhere, overlaying points from participating institutions, if so desired. Follow the instructions in red that appear on the screen. Enter your map's center and resolution using either latitude-longitude or UTM coordinates. The "fast" option uses cached data; the "all point" option queries the databases for their most recent updates.
  • Demo - Overlays kinds from databases at the Missouri Botanical Garden, University of Georgia, and University of Illinois onto maps and images. Click on the maps and images to zoom in. Click on individual points to retrieve information about them from the respective databases.

Browser requirements
The Global Mapper and Discover Life's reporting tool require your browser to support ISMAP. They work on all recent versions of Internet Explorer, Netscape, and Mozilla, except for Netscape version 4.79 on Mac's. Click here for more details and how to upgrade your browser.

Put maps on your site
You're welcome to put links to our global maps on your pages if you follow the HTML examples below which tell how. You do not need to contact us to seek permission.

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Checklists
The names in a checklist may differ from those listed when you press the identify button after starting a guide. Checklists do not list different morphs and sexes as do the guides. Checklists may include kinds that are not in the guide. A kind must have at least one character-state attribute to appear in the guide. Kinds that have yet to be scored and have no attributes only appear in the checklist.

Checklist are served to your browser as HTML. 20q builds HTML files from xml files. Use the following URL's to

  • View Lepidoptera checklist
    http://www.discoverlife.org/20/q?act=x_checklist&guide=Butterflies

When 20q refreshes a checklist, it shows in green what xml files it included in the html file and then displays the html file.

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Species and higher taxon pages

Link to our species and higher taxon pages with the following:

http://www.discoverlife.org/20/q?search=Genus+species (note the plus between the genus and species).

http://www.discoverlife.org/20/q?search=Genus

http://www.discoverlife.org/20/q?search=Higertaxon

For example,

<img src="http://www.discoverlife.org/favicon.jpg">
<a href="http://www.discoverlife.org/20/q?search=Trillium+undulatum">Trillium undulatum</a>

yields our icon and a link to our species page for this flower:

Trillium undulatum

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Listserve

Thanks to Sam Droege, on 2 September, 2005, the USGS started a listserve for us to share thoughts and ask questions about IDnature guides. It is called guidetalk.

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Import -- how to get information from your databases into our tools

Our goal is to enable you to use Discover Life's tools to process and share your information. The IDnature Guides (20q) and Record Manager (20l) have browser interfaces that enable contributors to enter and manage data manually via the Web. Here we discuss how to get information from databases into our tools. We consider

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File format
We import images, text tables, XML files, and HTML files using various utilities into our tools. Here we consider the simple case of importing tables. For more complicated cases, please contact our support center.

Importing tables
Our IDnature Guide, Image Center, Record Manager tools import ASCII text tables. They give data providers maximum flexibility and do not force them to use a rigorous data schema. Providers name and order fields that they wish to share. The tools index key fields, such as scientific name and geographic coordinates. They pass geographic information to the Global Mapper, which in turn combines data from all contributors into maps. They also integrate the information into the species pages served by the Search Box.

Here we describe how to format text tables from Excel, Access, and other databases so that we can import them. Each table requires the following format:

An example if a table with 4 columns that would plot two Quercus points in California:
___________________________
id$name$Latitude$Longitude
1$Quercus$37.8$-122.4
2$Quercus$33.5$-117.8
___________________________

An 8 column example:
___________________________
id$title$Latitude$Longitude$state$county$city$SourceURL^M
1$Golden Gate Bridge$37.81103$-122.47788$California$SanFrancisco$SanFrancisco$http://www.discoverlife.org Discover Life^M
2$Cresent Bay$33.54690$-117.80201$California$$Laguna Beach$http://whatever2...html Source^M
___________________________
Here we use Control-M to indicate the end of lines.
Note $$ in id=2, as no county for Long Beach is given.
Note the space after 'html' and before 'Source'.

Our tools treat certain fields in special ways. The following are used by the


Data transfer

We use the following options to transfer data:


Setting up new databases and automating updates

It is easy to import images and data into Discover Life. (Yeah, sure. Ha! Ha!)

This section is to help system operators working at Discover Life centers. While not quite black magic, it's not for data users, data providers, or the faint at heart. But no worries. By the time we've finished this documentation, the process may be automated and our operators out of a job.

Table name or URL:
If you have a single file to import, call the file $agent.txt, where $agent is your organization's unique code. $agents must be named with capital letters and no spaces; usually abbreviation of institution or database compiler

Thus, I_SB.txt is a valid filename.

This file can be put anywhere on the open Web. Alternatively, you can request an account on Discover Life and put it in your top directory.

Table format:
You must format tables as a text file with either tab or dollar signs separating fields. For details on formatting the file and the fields that it must contain see
File format above.

Crediting images and records:
Create a file called /home/IM/db/$agent/README to credit images and allow users to send feedback to data providers. The README file has the following lines:

For example see KSEM's README.

Formatting images to import:
Images must be formatted as a JPEG with file extension being in lowercase and the filename containing the $agent and a unique identifier (eg. I_SB98.jpg). If you can't rename your images with the $agent, we can do that for you, but you will have to assign a unique identifier to each image in the file name.

Steps are:

  1. Make the following subdirectories changing the permissions as stated:

  2. Editing agents file

  3. Creating nightly program

  4. Creating your .org file

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Scientific names

Discover Life and its partners manage over 1.2 million valid scientific species names and 440,000 other names on-line. These are associated with over 10,000 family names that are part of our Tree of Life, which is based on The National Science Foundation's Assembling the Tree of Life project. They can also be accessed via our search box and by browsing All Living Things.

We encourage taxonomists to contact us and use our tools to contribute and manage their scientific names, authorities, synonyms, references, and associated biological information. We also seek national, regional, and local checklists of names from surveys, inventories, and the published literature. We use such checklists to customize our IDnature guides by location at different geographical scales, including guides to local parks, nature centers, schools, and street addresses. We also add occurrence information from checklists to the maps displayed by the Global Mapper. As a free service, we use tools that reconcile checklist names with those in our authority files and provide feedback to our contributors so that they can update synonyms and correct misspellings.

Using the same valid scientific name across databases is essential to our collective efforts to link checklists, identification guides, photographs, catalogs, specimen records, maps, and other information into pages on species and higher taxa. In addition to managing valid names, synonyms, homonyms, and vernacular names, Discover Life has built tools to manage morphospecies, temporary names that help users in the process of identifying specimens and describing species.

Here are the rules that we follow in sharing names across databases.

  • NO ACCENTS -- Letters in scientific names are restricted to Latin A-Z and a-z. Although we support accents in authority names, in references, and elsewhere on Discover Life (see accents & symbols), our scientific names never have accented characters.
  • DATA STOREAGE VARIABLES -- We use up to three variables to STORE valid scientific names. These variables are $name, $morph, and $sex. We use an additional variable, $common_name, to store other names such as synonyms, alternative spellings, and vernacular names in different languages. We separate multiple synonyms and other names with semicolons within the $common_name variable. We use the variable $authority to STORE the author (and possible year and page combination) that ties a $name to its scientific reference. We use a final variable, $level, to specify the level of a $name, e. g., species, genus, and family.
  • IMPORT VARIABLES -- To support the vast array of non-standard taxonomic databases, we do not require contributors to have their data in any particular format. We have a large number of translators that IMPORT data into the storage variables described above. For example, many taxonomists keep $genus and $species variables as separate columns in their spreadsheet and database tables. For species level names, our translators combine $genus and $species and store the binomial in $name, separating the genus and species with a space.
  • VALID HIGHER TAXA -- Valid genera and higher taxa always start with a capital A-Z and have one or more lowercase letters a-z. They contain no spaces or accents and are stored in $name.
  • VALID SPECIES -- A valid species name is a binomial with a valid genus and specific name. The specific name is all lowercase a-z but may include a hyphen '-', e. g., 'Smilax bona-nox'. There is a single space between the two names. It is stored in $name.
  • NEW GENERA -- Unpublished, new genera start with the convention 'Gn_' (capital-G lowercase-n underscore) and then follow the rules of morphospecies below which separate them into a unique, temporary generic names.
  • MORPHOSPECIES -- Morphospecies names are temporary, working names that are stored as binomials in $name. The second, specific name must start with 'sp_' (lowercase-s lowercase-p underscore) and be followed by a unique investigator-place-project-number combination which distiguishes it from other morphospecies, e. g., 'Rogas sp_Panama_3' or 'Rogas sp_UGCA_5'. Use underscores, not spaces to separate words. Put 'sp_' before 'cf', 'nr', 'n_sp', 'near' and other ways of describing morphospecies, e. g., use 'Jornandes sp_n_sp_from_chiapas' or 'Scalponotatus sp_nr_chilcotti_2'. After the 'Gn_' and 'sp_' you may use these characters: A-Z, a-z, 0-9, _. No other characters, including spaces, periods, parentheses, commas, colons, question marks, quotation marks, and apostropies are allowed.
    Correct example: sp_Costa_Rica_black_and_red_1
    Incorrect example: sp_Joe's new black & red sp. nr. whatever
          (apostrophy, ampersand, spaces, and periods are not supported)
    In some cases, we adjust morphospecies names which are not formulated with 'sp_' as described above, e.g., 'Genus sp.' & 'Genus spp.' are changed to 'Genus', dropping the 'sp.' or 'spp' after the genus. In some cases, we recommend renaming these a supported morphospecies name, such as 'Genus sp_1'.
    In using 'Gn_' and 'sp_' in temporary names, Discover Life's tools rank morphospecies into the following three levels:
    1. Equivalent to valid species: By adding a morphospecies to one of our authority files via an IDnature guide or checklist, the morphospecies will be treated as if it were a valid scientific binomial. It will appear in the list of species on the genus page. Specimen occurrences will also map with the genus.
    2. Within a location checklist: By adding a morphospecies to a location checklist (but not to an authority file as above), images of the morphospecies will appear with other species in the list. This feature helps local projects display specimens of morphospecies that they have grouped together but have yet to identify to a valid species. These morphospecies are not listed on generic pages. They map when specified by their name; map when their genus is specified, but do not map as a species when the genus is specified with a trailing underscore (e. g., 'Palpita_').
    3. Within a sorting category: By making the first letter of the genus or highertaxon of a morphospecies a lowercase letter, e. g., "moth sp_near_palpita_maritima", one can create sorting categories that are listed in a site's 'Table 3. Sorting categories'. These morphospecies are invisible to the mapper, except by mapping them via their unique identifiers.
  • SUBSPECIES, VARIETIES, FORMA, AND HYBRIDS -- The variable $name links to a web page. It CANNOT be a trinomial with two spaces. There are two ways to store information about subspecies, varieties and forma.
    • Option-1 [preferred] -- use the $morph variable
      If we import the name of a subspecies, variety, etc. into the $morph variable, then it will be associated with the species page to which it is a member. There are on-line tools within the IDnature guides for managing information associated with the $morph and $sex variables.
    • Option-2 -- append the third name after an underscore to the end of the $name variable
      This option separates the kind from its species and gives it a page under the genus.
      • Subspecies: use 'Genus species_subspecies', e. g., 'Wasmannia auropunctata_australis'.
      • Variety: use 'Genus alpha_var_beta'.
      • Forma: use 'Genus alpha_forma_beta'.
      • Hybrids: use 'Genus alpha_x_beta'.
  • HOMONYMS -- In the case of homonyms, as a temporary measure, we append '_homonym' to one $name to distiguish it from another taxon with the same name, e. g., Cepolidae and Cepolidae_homonym, which we use as fish and gastropod family names, respectively. Use '_homonym1', etc., if necessary.
  • TAXONOMIC AUTHORITY FILES -- Our taxonomic authority files associate species with higher taxa and take precedence over other information on names. Contributing taxonomists can import and manage these files with the IDnature guide (20q) software. The databases that manage images and maps use these authority files to associate species with higher taxa. They do not contribute to the authority files. BE WARNED that if a species is in a map database, it will NOT map as a member of a genus unless the species is also a member of the genus within an authority file. While this may seem inconvenient, it keeps a large number of spelling errors within map and image databases from creating bogus species within genera.
  • IMAGE TITLE -- We use an image 'title' to associate images with species pages, maps, and graphs. To do this, the title value should start with a valid scientific name. It may have additional information after a comma. For example, 'Solenopsis invicata, queen, head' will associate the image with Solenopsis invicta's species page.

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Labels
20q links to a labelling sytem, 20l. As of 24 February, 2003, this labelling system uses the following XML schema:

<parent id="$id" gmt="$when_gmt" ip="$ip">
<latitude> $la </latitude><longitude> $lo </longitude><accuracy> $accuracy </accuracy><elevation> $elevation </elevation>
<country> $country </country><state> $state </state><county> $county </county>
<city> $city </city><site> $site </site><position> $position </position>
<time1> $time1 </time1><time2> $time2 </time2><days> $days </days>
<who> $who </who><email> $email </email>
<how0> $how0 </how0><how1> $how1 </how1><how2> $how2 </how2>
<how3> $how3 </how3><how4> $how4 </how4>
<habitat> $habitat </habitat><field_note> $field_note </field_note> <note> $note </note>
</parent>

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Browsers

Discover Life's 20q software supports most recent browsers, including Internet Explorer version 4, Netscape version 6, and Mozilla version 1.0.2. There are a few bugs in recent versions of Internet Explorer (version 5 needs Flash) and Netscape (version 6 under Mac OS X) that cause some images not to appear in full color or at high resolutions. If you have problems, try using IE 4, which works on Windows and Mac platforms. Netscape 4 has problems with our interactive maps on Macs but version 4.7.6 works under Windows. Map targets do not display on any IE or Netscape version 3 or below.

If you need to upgrade your browser, click here to upgrade to Firefox.

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File transfer -- download ssh & scp

If you are a data provider with an account on Discover Life, you will need ssh/scp communications software to login to our firewalls (pick2.pick.uga.edu or pick9.pick.uga.edu) and transfer files. ssh lets you run commands on Discover Life servers. scp allows you to transfer files back and forth. For security reasons, we no longer support older protocols such as telnet and ftp.

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Disclaimer
We make no guarantees to the accuracy of IDnature guides. If you find errors, please report them to us.

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Contact us
Please send your suggestions of how this software and guide can be improved to
John Pickering.

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