Contributors

The eMonocot portal aggregates data from a number of expert communities and other resources into a single place. This section explains how you can contribute information to the eMonocot portal.

General Information

Q. Who can contribute information to eMonocot?

A. Anyone publishing information about monocots can contribute their information to eMonocot. There are a number of existing expert communities that contribute data and generally we would recommend that you try to join an existing community if there is one. eMonocot is attempting to deliver a community-based consensus taxonomy, so we wish to avoid multiple, overlapping resources. If there is no expert community that is appropriate, we recommend that you start one. The eMonocot team will try to assist you where we can.

Q. What kinds of information can I contribute to eMonocot?

A. The eMonocot portal can accept information about taxonomy, nomenclature, descriptions, distributional information, references, identifiers, specimens, vernacular names and measurements or facts. We require this information to be published as a Darwin Core Archive, and made available via the web. In addition, we accept identification keys provided as Structured Descriptive Data (SDD) and phylogenetic trees provided as Newick, New Hampshire Extended, NEXUS, or PhyloXML, again made available via the web. Specific information on each of these formats is provided below.

Q. Are there any tools or programs which I can use to assemble and manage this information?

A. If you don't already have a database or other system for managing your taxonomic information, we recommend using a Scratchpad. Scratchpads are a web-based tool that allow communities of taxonomists to publish taxonomic information online. Scratchpads can be configured to publish data as a Darwin Core Archive automatically. However, you can use any other means of creating a Darwin Core Archive, including using readily available office software such as Microsoft Excel, and file compression tools to create the zip file. Identification keys can be created using Lucid Builder, Xper2 and can be converted from other formats such as DELTA into SDD. Phylogenetic trees can be created using a variety of open-source software packages.

Archives and other files can be made available on a private or institutional web server, or you can use other programs such as dropbox, google drive, or the internet archive to make your data available to the eMonocot portal.

Q. I don't want to make my information available to everyone on the internet! How can I provide information to eMonocot?

A. The simplest way is to use some kind of access control to restrict who can access your information. Your systems administrator may be able to help with this. Please remember to allow access to the eMonocot harvester (zoo-bclark02.zoo.ox.ac.uk) if you want to provide data to eMonocot.

Q.  I have content that I wish to contribute to eMonocot what should I do next?

A. First, find out if there is an existing community, and if so, join that community and contribute content to it. If you cannot find an appropriate community to join, consider starting your own.

Q.  How do I find out what eMonocot Scratchpad communities exist?

A. Look at the list of eMonocot Scratchpads.

Q.  How do I  join an existing eMonocot Scratchpad community?

A. Each scratchpad has a "Log in" link at the top of the page. Selecting this link gives you the option to "Create a new account". Once you have an account, you may need to contact the maintainer of the scratchpad to be allowed to create and edit pages (at the discretion of the maintainer).

Q. How do I start my own eMonocot scratchpad?

A. Visit get.scratchpads.eu. Remember to ask for an eMonocot Scratchpad if you want an eMonocot Scratchpad instead of a default Scratchpad.

Q. I do not want to manage an online taxonomic resource can I still contribute content e.g. images, Keys, pdf publications?

A. eMonocot aggregates content from curated resources - please consider contributing your content to an appropriate expert community.

Identification Keys

Q. How do I make a key available to eMonocot?

A. Keys should be made available as Structured Descriptive Data, an XML schema which can be exported from common key-building programs such as Xper2 or Lucid Builder. The XML file should be made available via the web.

Q. Can I provide an illustrated key to eMonocot?

A. Any images included in the key should be published online. Most key building programs will include the local path to the image (e.g. file:///c:/Users/Username/Documents/MyKey/Image.png). This should be changed to the web-address of the image in the SDD file (e.g. http://example.com/MyKey/Image.png).

For example

<Source href="file:///c:/Users/Username/Documents/MyKey/Image.png"/>

should be changed to

<Source href="http://example.com/MyKey/Image.png"/>

Given that most key building programs organize images in a single directory, a single global find and replace (often CTRL-H in a text editor like Wordpad) is sufficient to convert a key.

Images need not be listed in the Darwin Core Archive images extension file associated with your organization. If they are not, they will be deleted when the archive is imported. You will need to import the key again in order to import the images. The best situation is for images to be listed in a Darwin Core Archive so that this re-import is not required.

Images associated with taxa are not displayed in the key. Images associated with Characters, Descriptive Concepts and States are displayed in the key.

Q. How should I label the taxa / entities in my key?

A. Most key building programs do not use globally unique identifiers to identify taxa. Consequently eMonocot matches the label of the entity to the taxa within eMonocot. Please include the full scientific name of the taxon. For example, species should include both the generic part and the specific epithet. Supra-specific taxa should only include the uninomial. The authority is allowed, but not required - it will be useful in the case of homoynms. If the portal cannot match a name exactly, this name will be included in the key but not linked to a taxon page. An error will be listed in the job report.

Including other text in the entity label is discouraged as this will prevent the portal matching the entity.

Taxonomic Information

Q. How do I make taxonomic information available to eMonocot?

A. Most information should be made available as a Darwin Core Archive. We require that:

  1. There be a single core file containing objects of type dwc:Taxon
  2. Optionally, there be extension files containing information of following types

Please review this technical documentation to find out what properties are allowed. In general all properties in the GBIF specifications are allowed. Some additional properties are permitted but not required. Other optional properties are ignored by eMonocot (not imported). Machine-readable technical documentation is available here.

Properties that are text are usually restricted to 255 characters, with the exception of dc:description and dc:rights fields which can be longer. Text fields may contain markup, but markup will be filtered to remove some tags and attributes. Formatting tags (em, strong, i, u, b, sub, sup), ordered and unordered lists (<ul><li></li></ul> / <ol><li></li></ol>), quotes (<q></q> / <blockquote></blockquote>), paragraph (<p>), break (<br>) and horizontal rule (<hr/>) tags are allowed.

Links (<a href="link">text</a>) are allowed if the link is global (i.e. relative links are filtered out).

Attributes such as class and style are filtered.

Rows which contain problematic values are not imported, and an error message is displayed in the job report. If an archive contains a large number of problematic rows, the harvesting job may fail.

Phylogenetic Trees

Q. How can I provide a phylogenetic tree to eMonocot?

A. eMonocot can harvest phylogenetic trees as Newick (*.nwk), New Hampshire Extended (*.nhx) , NEXUS (*.nex) or PhyloXML (*.xml). Only the first phylogeny in a given file will be imported. If branch lengths are included they will be used, otherwise branch lengths are assumed to be equal.

Q. How should I label the OTU's in my phylogeny?

A. Most phylogeny building programs do not use globally unique identifiers to identify taxa. Consequently eMonocot matches the label of the OTU to the taxa within eMonocot. Please include the full scientific name of the taxon. For example, species should include both the generic part and the specific epithet. Supra-specific taxa should only include the uninomial. The authority is allowed, but not required - it will be useful in the case of homoynms. If the portal cannot match a name exactly, this name will be included in the phylogeny but not linked to a taxon page. An error will be listed in the job report.

Including other text in the entity label is discouraged as this will prevent the portal matching the OTU.

Q. How do I add a new phylogeny to eMonocot?

A. Every phylogeny in the portal has to be created as a resource of an organisation. If there is not an organisation suitable for the resources you are adding create a new one (see here how). Once logged in, from the organisation page, select 'Create a new resource' and fill the required fields.

Resource Name Name of the phylogeny
Url Link to the original resource (eg. a .nex file) of the phylogeny
Type

Select PHYLOGENETIC_TREE from the drop-down menu

Select 'Submit' to save it. You'll be redirected to the summary page listing all the resources in the portal. Search for your new resources (eg. searching for the resource name or filtering the list) and click on its name. You'll access to the resource page. You can at this point edit the resource with the remaining information needed. Don't edit the field in the form. Instead go to the bottom of the page to add new parameters.

The parameter to add are:

Parameter Name Parameter Value
root.taxon.identifier eMonocot identifier of the reference taxon for the phylogeny (eg. urn:kew.org:wcs:taxon:239724)
input.file.extension The phylogeny file extension (eg. nex)
phylogeny.creator The Phylogeny main author
family The phylogeny family (Note: add this parameter only if all the taxa in the phylogeny belong to the family)
phylogeny.title The phylogeny title
phylogeny.description Description styled as: Authors, Year, Title, Journal, Pages.

Note: Insert in the parameter field only the parameter name. You will add its value only after you added the parameter to the form.

Images

Q. How can I provide images to eMonocot?

A. Images must be available over the network for eMonocot to harvest them (via HTTP). Images can either be referenced in a Darwin Core Archive (using a gbif:Image extension file) or from an Identification Key (as an sdd:MediaObject).

Q. How do I provide metadata about my images?

A. eMonocot will harvest metadata from an external file (either the gbif:Image or sdd:MediaObject) by preference. If metadata of a give type is not available, we can also import metadata that is embedded within the image itself. The table below shows how individual fields are mapped to the gbif:Image standard

  TIFF / EXIF IPTC XMP
dc:Title   Object Name dc:Title
dc:Description TIFF:Image Description   dc:Description
dc:Subject   Keywords dc:Subject
dc:Creator TIFF:Artist   dc:Creator
dc:Format     dc:Format
dc:Spatial   Sublocation, Province/State, Country/Primary Location Name iptc:Location, photoshop:State, photoshop:Country
dc:Created     photoshop:DateCreated
dc:Rights TIFF:Copyright   xmpRights:Copyright
dc:RightsHolder     xmpRights:Owner
dc:License     xmpRights:UsageTerms, xmpRights:WebStatement
wgs84_pos#longitude EXIF:GPS    
wgs84_pos#lattitude EXIF:GPS    

Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith