polychaetes.info

This website is a project outcome of a polychaete workshop held at the Natural History Museum in January 2007, sponsored by Census of the Diversity of Abyssal Marine Life (CeDAMar), a field program of the Census of Marine Life. Our goal was to create a simple to use system to exchange taxonomic data (descriptions, images etc.) over the internet between working groups. For example, there are probably a handful of people in the world working on abyssal (and/or deep-sea) Cirratulidae, generating their own species data and morphological datasets. We wanted to create a system to make it easier for them to collaborate using a 'Web 2.0' style collaborative authoring and networking system. Essentially, a system to allow users to upload information on a species they are working on, and allow other users to comment on it.

At the same time we were thinking about this, a web taxonomy project called the European Distributed Institute of Taxonomy was being established by a group of researchers interested in using the web for exchanging taxonomic information. We seemed to be exactly the sort of user group they were looking for, so we have developed a site based around their content management system, called Drupal. This site is hosted by EDIT and is being maintained with their assistance, however, the design of the site and how it is developed is essentially left to the site maintainer, currently Adrian Glover at the Natural History Museum.

The EDIT sites are intended to be 'scratchpads' for taxonomic user groups. In fact, the capabilities of the system go quite a way beyond what we originally envisaged. In essence, this is a 'wikipedia-style' database of entries on polychaete families, genera, species and species records from abyssal and deep-water sites. Users can include descriptions (in easy-to-edit free text areas), images, information on type or voucher specimens, GenBank accession numbers, and geo-referenced locality data that is automatically mapped using a google map module.

Anybody can view the data, images, descriptions and other content on the site, using the search tool, the taxonomy browser tool (a tree, generated on-the-fly from taxonomic names databased on the system), or by clicking through recent posts in the news feed - Recent Posts.

However, unlike 'wikipedia-style' databases, only registered users can comment on, edit and post their own data. To become a registered user, you need to get a user id.

2. Getting a user id

You can apply here . You will be assigned initially as contributor status after admin approval.

Contributors can see all the content and upload their own descriptions, images and data, and comment on others.

Editors can do all the above and edit other peoples data.

You will need to sign (just one click) a form saying that you take responsibility etc. for the content you put on the site.

3. Viewing content and resources

When you are not logged in, you can see all the resources, taxonomy browser, links, search form etc. However, when you are logged in, you can also access the special content creation menu called Actions.

Resources menu

Discussion forum: you can post forum topics and contribute to discussions here. Fairly self explanatory.

Polychaete records map: this is a live map that is updated as people enter species records and descriptions into the APOL database. It is a google map module that should be fairly familiar, with the usual controls to view the whole world on your screen. Hovering the mouse button over a marker will display the species record name.

User location map: this shows the location of registered users of the site on a google map module.

Fileshare: this is a useful area to post large files you want to share with other users. Fairly self-explanatory.

Taxonomy browser

The taxonomy browser is one way to browse the data on the site. It is based on a very large (many thousand) list of taxonomic names that we have extracted from ITIS and species2000. The classification may not be the most up-to-date, but the important thing is to get a list of names that are a crucial part of the database. You can browse this taxonomy by clicking on the names, which expand as you click them. The small blue plus-sign next to a name are the links that allow you to see any data users have entered that is associated with that name. For example, if you navigate to the genus Chaetozone, and click on the blue plus, you will see all Chaetozone species that have been entered on the site.

This taxonomic tree goes right to species level, but of course there are some names missing. Users can add names (making sure they place them in the right part of the tree!) using the Create/Edit Taxonomic name button, under the Actions menu. More on that below.

Actions

These are things you can do, as a registered contributor or editor on the site.

Create family description: a form to fill out if you want to add information on a family, for example a family diagnosis for a new family. I do not think this will be used very much, but it is there if you want it.

Create genus description: a similar kind of form to the family one, but with some more fields. This may be used more often as there are quite a few deep-sea genera awaiting description or revision. You can add an informal description here, e.g 'NewGenus_A'.

Create species description: this is probably one of the more important things you can do. You have a new species you want to describe on the internet, but not as a formal publication. You can add it here, so that other users can see it and comment. They could even post their own records of this species using the species record form.

Create species record: this content type is organised into three sections - the sample, the specimen and the taxonomy. This content type is to report a finding of a published, or unpublished (but perhaps published on this site) species. Again, this should be fairly self-explanatory, and the run-through of the fields in the species description content type below should aid you.

Create/Edit taxonomic name: this button should be approached with caution. All contributors will have the opportunity to input names into the taxonomic database here, but it is crucial that these are accurately spelled and placed in the correct 'parent'. For example, I recently discovered that the name Aurospio was not in the taxonomic terms, so I added it with the parent 'Spionidae'. Fairly simple, but one slow part is scrolling through the long list of names to find the parent. We are working to make this easier. Remember, that unless your species description is tagged with a taxonomy field name, it will not appear in this tree. Although you can still search for it, and it will still appear in the news feed.

Note: none of the data you enter on this site is a formal taxonomic description, none of it adheres to the current rules of the ICZN.

Links

This area just contains useful links.

<your username>

This is a navigation part of the site that is specific to you. It is not super-intuitive, but you should be able to find things such as your account details if you want to change your password, that sort of thing.

Search

You can search the entire site using this feature. E.g if you want to find everything related to the genus 'Chaetozone' type it in here.

Statistics, Who's Online

This is fairly self explanatory.

Recent Posts

This area shows all the most recent content that is posted or edited within the polychaetes.info site.

News from Nature

This is just a news feed from Nature magazine.

4. Creating species description content

I will go over the process of creating a species description. If you can understand that, you will be able to understand the species record, family and genus content types too, as there are many commonalities.

Click on Create Species Description under Actions. You will see a form to fill out, most of which has help text. There are a few less obvious things which I will also mention here.

The first field is Species Name. You will see an orange star next to it, indicating it is a required field. You can enter whatever text you want here. E.g. 'Chaetozone sp. A' or 'Cirratulid with long palps' or Chaetozone setosa, an actual name. This field is the title of the content you are creating so it is important. But it is not the name used in the Taxonomy Browser.

Uploader is you, the user.

The next section is the 'Systematics' section of your description.

Taxonomy is the all-important field that you must get right. You must only enter terms here that are in the list of names. For example, if you are putting in a new species called 'Chaetozone sp. A' you must enter just the actual published name which in this case is Chaetozone. Just start typing the name and a list should appear below the field, select the correct one. If your species is not in the list, you must add it using the Create/Edit Taxonomic Name command, under Actions.

Species name (informal) this is another field which basically, should be the same as your Species name entered as the title. For various reasons, this is needed again here.

Continuing down the form, everything should be fairly self-explanatory. You will eventually reach the Attached Images function. You must click on this if you want to attach an image, obviously. When you do, you can attach an image that is already on the database (unlikely) or choose one on your computer using the browse command.

Note on images: at the moment, you can only attach 1 image per record with this function. This will be changed in the future, but for the moment if you want to show several images, you should arrange them as a 'plate' using a program such as Adobe Photoshop, as in this example. Your image must be less than 2mb in size, and I recommend you make it smaller for quick download. An image that is 1000 pixels wide (approx), less than 1mb is ideal. You need to use standard image formats such as JPG, PNG, GIF etc, obviously.

Location: this is the google mapping module. You must enter a Lat/Long here for the voucher or type specimen using a decimal lat long system, with anything that is S or E designated with a negative sign. e.g Lat: -10.2 Long; 50.5 should be entered if your position is 10°12'S 50°30'E. Unless your lat/long is entered here correctly, you will not see your species on the map! Please take the effort to input your lat/long. Once you have typed the data in, gmap will map it straight away so you can check it is correct. You can also enter locations just by clicking and dragging in the map window, although this will be less accurate.

That's it. You can now press 'submit' and your species description is on the web. All data on this site is maintained at the Natural History Museum, London and backed up on a daily basis by the EDIT team.

5. Editing the taxonomic names

Under 'Actions', you can create/edit the taxonomic names used by the site. This is very important, as these names are the tags for the species description and record content types. By tagging your descriptions with the right name, your description will be accessible by browsing the taxonomic tree. If you do not tag it, it will be harder to find, but you can still search for it.

If you have a name you want to add, or edit, click on the create/edit taxonomic name link.

You will see a long list of names organised in a hierarchical fashion. To add a new name (term), click Add Term. Unfortunately there is no easy way at present to search this list (we are working on this!). There are only two things you must fill out. The 'Parent' and the Term Name. For example, if you want to add the genus Monticellina then you would click on Parent, find and select 'Cirratulidae' and then add Monticellina (spelled correctly!) to the Term Name field, and click submit - that's it. Ignore the other fields.

In the term list, you can also edit existing terms (e.g moving a genus from one family into another, or fixing a spelling mistake). Unfortunately, it is not easy to search or browse the list, you have to go through it manually to find the term to edit. We are working on this.

6. Quality control and peer review

It is expected that for the moment, any new users we create will also be editors. That is, they can edit other people's content. In the same way as wikipedia, quality and accuracy will be maintained by the user community editing each other's content. This is an experiment, and we are not yet suggesting that this is the best way to make the site work. However, studies have shown that the collaborative authoring approach is best achieved by harnessing the power of many. In other words, we do not want to create the bottleneck of just one or two editors.

7. Commenting and discussing content

Most areas of the site are commentable. This means you can post a comment, even an image, for all to see. This should be most valuable on the species content type pages, where you can post comments on the taxonomy. A discussion forum could easily be started on spionid morphology for example.

6. Future developments

As you will see in the forms, the morphological data is entered in free text areas. Of course, it would be possible to create a far more advanced database, with an enormous range of fields allowing us to enter the morphological data split into separate fields, as in the programs DELTA and LUCID. At the moment, this is beyond our capabilities. If you have DELTA descriptions, it is fairly easy to paste them in. The EDIT team are looking at ways to import these data directly in the future. This could be something we could explore. It would also allow for online keys to be automatically created, a development that many would find very useful.

Another area we will develop is more ways of viewing the data. It would be very easy to create tabular views showing species lists, localities etc. that are updated on-the-fly. This will be done soon, once there is some data to view.

I have not included any special molecular fields other than an area to insert GenBank accession numbers. NCBI can take care of that data.

7. Geting help

There is no 24 hr telephone support! Please experiment with the site and try and figure out a way around your problem before contacting the site maintainer, currently Adrian Glover at the Natural History Museum.