Users

A guide for all the users of eMonocot portal

Identification key

Q. Who can edit information about an existing key?

A. Identification keys are a type of resource, so they are managed as any other resource. Metadata about a key such as its creator or title is provided in the SDD file by the key publisher.

Q. What does 'Prune redundant' (characters) mean?

A. If you select 'Prune redundant', the characters that do not discriminate the remaining taxa will be hidden from the available feature list. Once you have selected another character from the restricted list of characters, some remaining characters may be redundant, so selecting 'prune redundant' a second time may remove more redundant characters.

Q. What does 'Next best' (character) mean?

A. This button allows you to select the features in a more efficient way, suggesting to you the character that will discriminate best between the remaining taxa.

Classification

Q. The right click doesn't allow me to open a node link in a new browser tab/windows. Is there an alternative way to do that?

A. The right click is not working in the classification tree. You can still open a link in a new tab/window using the usual keyboard combination for that.

  New tab New window
Mac CMD + click SHIFT + click
Windows CTRL + click SHIFT + click


Phylogenetic trees

Q. Who can edit information about an existing phylogenetic tree?

A. Phylogenetic trees are a type of resource, so they are managed as any other resource. Information about a phylogenetic tree is provided in the resource file itself, or as parameters in the resource record in the portal. Only administrators can edit a resource.

Taxon

Q.  What is a taxon page and which information does it contain?

A. A taxon is a general term denoting a named group of organisms of any rank (e.g. variety, species, genus, family). All the available information about a specific taxon are collected in the related page in the portal. 

Comments

Q. Who can post a comment?

A. Any registered user can post a comment once logged in.

Q. What can I comment on?

A. Comments are available for Identification keys, Phylogenies, Taxon pages, Images and Terms.

Q. What happens once I submit a comment?

A. Once submitted, your comment will be posted in the eMonocot portal. It will be visible in the specific page you commented on, in the portal home page (that shows the latest comments) and in the general comment page (www.e-monocot.org/comment). In the page you can see all the comments submitted in the portal, search them by any word, or restricting them by family, subject or content type. Your comment is also sent to the owner of the resource you commented on.

Q. Who manages the comments?

A. Comments are not moderated. Administrators may delete comments.

Q. Where can I see all the comments?

A. There is a general comment page available to all the users at www.e-monocotorg/comment. You can search for terms in the comment or restrict  the comment list using the filters on the left. You can also see the comments in the page they are related to.

Download

Q. Who can download content from the portal?

A. Any registered user can download content, provided they are logged in.

Q. What type of content can be downloaded?

A. Once logged in, you can download information on taxa and phylogeny. No download is available for the other result types.

Q.  How do I download information?

A. You can download information from two places

  • Taxa: in the search and map(spatial) search pages, you need to restrict your search to only taxa in order to download them.
  • Phylogeny: You can download them directly from the phylogeny page.

Q. In which format will the data be downloaded?

A. There are two available type:

  • Structured data is available as a delimited file (Taxon File Only) or an archive containing a Taxon File plus related information in a Darwin Core Archive.
  • Formatted data  ('Alphabetical Taxon List' and 'Checklist of accepted taxa containing publication information and synonyms').

Q. Why is the number of results listed in the search different from the number of results in the download? Why are some data missing from the download?

A. The number of records you download may differ with the download format and providers' restrictions. Data which is not licensed for redistribution will not be included in a download.

Organisations

Q. What is an organisation?

A. An organisation is a person or a group of people that owns data. It's the source of the data in the portal.

Q. Who can create a new organisation?

A. An administrator can create a new organisation.

Q. Who can edit an organisation?

A. The any member of a group with the correct permissions can edit a resource, once logged in. Typically the owner of an organisation will be given permission to edit the organisation.

Resources

Q. What is a resource?

A. A resource is a file which can be harvested into the portal. It always belongs to an organisation.

Q. Which are the type of resources?

A. There are three main types of resource, and two types associated with specific organisations.

  • DWCA - a  Darwin Core Archive.
  • Identification Key - Is an xml file containing the data defining a multi-access key (as SDD).
  • Phylogenetic tree - A text file containing a phylogenetic tree as NEXUS, Newick, New Hampshire Extended or PhyloXML.
  • GBIF - Global Biodiversity Information Facility - An xml file either downloaded manually from the GBIF data portal or provided by their RESTful web services
  • IUCN - International Union for Conservation of Nature - A response from the IUCN Red List API

Q. Who can create a new resource?

A. Only administrators of the portal can create a new resource.

Q. Who can edit a resource?

A. Only administrators of the portal can edit a resource.

Q. Who can browse the resources and access to the harvest report?

A. Anyone can browse the resources, and filter the list according to different categories (Exit code, Resource type, Scheduled, Scheduling period, Status. Organisation, Last harvested). All the users can also access to the harvest report.

Q. What information does the report contain?

A. The report contains information about the output of an harvest job. You can filter the report according to the data type and the category of the output. You can also search by any word appearing in the output.

Report summary
Category Sub category Details Record
Error Bad Field Some fields are required for a particular record type (for example, Distribution records must have a locationID). This category of error is thrown when a required field is empty Link to the record page in the portal.
Error Bad Identifier An identifier for another object (usually a taxon) is present but not found in the portal. Occurs when records are linked to taxa which are not harvested or when a taxon has been deleted from the portal but not the source system.  
Error Wrong Authority The job has tried to update an object but the record in the portal was originally harvested from another system - can occur when e.g. images in the family scratchpad are included in other keys (and the key was harvested prior to the family scratchpad harvesting)  
Error Bad Record A field in the record contains an invalid value. Examples include fields which should contain values from a controlled vocabulary, or values which exceed the maximum allowed size for that field.  
Warn Absent A taxon record was expected in the resource but was not found. Occurs when a resource is not in sync with the authority for that taxonomic group. Link to the page in the portal corresponding to a missing record in the resource.
Warn Unexpected A taxon record was found in the resource but it was not expected. Occurs when a resource contains taxa which (according to the portal) do not belong to the group the resource covers.  
Info Create The record has been created in the portal. Link to the page in the portal containing the new record.
Info Present A taxon record was expected to be in the archive and was found. Link to the page in the portal containing the existing record.
Info Update The record has been updated in the portal. Link to the page in the portal with the updated version of the record.

Registration

Q. Who can register in the portal?

A. Any user register in the portal. It is free to register.

Q. Why should I register to e-monocot?

A. All of the content in eMonocot is available without registration, but there are some features which are restricted to registered users. If you would like to download data for use offline, download a pdf checklist, or if you would like to send feedback to the people who curate the data in eMonocot, you need to create an account.

Q. How can I register?

A. In order to register in the portal, click on the 'Sign in' button on the header. You'll be redirected to the general login page (www.e-monocot.org/login). Click on 'Create new account' and fill the registration form

Q. What happens once I register?

A. An email will be sent to the email address you provided with a one-time-only link. Selecting the link and following the instructions will activate your account.

Q. What is the ‘API key’ field in the profile page?

A. The api key is a unique string which you can use to authenticate yourself when using the eMonocot API. See the developers guide for more information on the API.

User page

Groups

Q. What is a group?

A. A group is used to grant users special permissions in the portal (for example, to edit a particular organisation).

Q. Who can create a new group?

A. Only administrators, once logged in, can create a new group.

Q. How can I be part of a group?

A. To be part of a group, you need to email 'enquiries@e-monocot.org' asking to be added to the group you are interested in.

Q. What is the 'Access Control List'?

A. An ‘Access control list’ is a list of permission attached to a group. It specifies which users are granted access to a group and which operations are allowed on that group.

Recovery

Q. I forgot my password. How can I restore it?

A. In the login page, click on the "Can't access your account?" link and insert your email address. You'll receive an email from eMonocot with a link you can use to reset the password.

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