What is a category page? What is a page?
The NeuroLex is built using something called the Semantic MediaWiki. We chose this platform because it makes it easier to go between the formal ontologies and the Wiki space. It can be a little confusing to get started and to understand its structure. We have created several video tutorials explaining the structure of the NeuroLex and how to edit it. These tutorials are available from the page, How to Contribute to the NeuroLex. We'll be adding more in the future.
How are categories related to one another in NeuroLex?
NeuroLex was designed as a single tree hierarchy, that is, a given category has one and only one parent category (super category) and one or more children categories. A category is related to its parent and children through a "is a type of" relationship, also called an "is a" relationship. So, a Neuron "is a type of" Cell; a "Purkinje cell" is a type of" Neuron. In order to make sure that each Category is related to its parent only through an "is a" relationship, NeuroLex has created some contrived categories, e.g., Regional part of brain; Cytoarchitectural part of hippocampal formation". We are preparing some additional documents to provide the rationale for this design, but for now, they provide useful buckets into which we can place information. The next phase will be more tricky, as we define other relationships between categories that are necessary to build a network of neuroscience concepts. The NeuroLex lets you define other relationships between Categories, e.g., "Is part of"; "Located in"; "Neurotransmitter". For a list of these properties, please see Special pages. When you are defining relationships between categories, you should make sure that you use the correct relationship. The easiest way to do this, is to create a sentence with a subject (Category 1) a predicate (relationship) and an object (Category 2). The Thalamus "is part of" the Diencephalon.
How do I add a new class?
You can find a quick start guide here.
How is the NeuroLex different from Wikipedia or any other Wiki-based encyclopedia for neuroscience?
The NeuroLex is interested in defining the meaning of concepts of use to neuroscience in a way that is machine processable. Neurolex does not provide general or interesting information about the concept. It is more of a dictionary than an encyclopedia, concentrating on the meaning of the terms that neuroscientists use to describe the nervous system. We also don't focus just on notable concepts, but on any concept a researcher uses to describe their data. The purpose of the Neurolex is to create this information in a way that is "machine readable". Thus, we rely on formal properties as a means of defining and linking concepts. We want to make explicit the way in which a concept is defined so that it can be consistently applied to data annotation. Neurolex thus becomes a computable index into neuroscience data, via the Neuroscience Information Framework, as well as knowledge base unto itself. We aren't interested in creating the "right" definition of a term like basal ganglia, but to allow the community to tell us the many ways in which it is defined. Thus, we have created a definition template and some policies that allows the user to provide the required information in a form that's easy for automated agents to understand.
Do I need an account to contribute to the NeuroLex?
No, you do not need an account. We want the NeuroLex to provide a very low barrier entry point for you to contribute your knowledge. We view the NeuroLex as the marketplace of ideas for neuroscience concepts. However, if you do get an account, all of your contributions will be linked to you.
Is NeuroLex curated?
Yes, it is. We monitor the NeuroLex regularly. Some of the content of the NeuroLex is already being incorporated into our ontologies by knowledge engineers working on the NIF. We will certainly remove any content that is inappropriate (i.e., doesn't fall within our scope, is obscene or inflammatory). We will also update entries that have been incorporated into the NIFSTD ontologies so that the concept can recieve an appropriate version number. But the NeuroLex is meant to be a community resource and needs to evolve in a way that is useful to the community. So we will adjust our curation policies if necessary as we go.
What are some best practices for defining my new term?
The primary purpose of terms in Neurolex is for the annotation of data. Therefore, the definition should provide the meaning of the term in a way that distinguishes it from other related terms (monothetic) so that users will know how to apply that term to their data. We favor the Aristotelian approach: A "is a type of" B "which has" C. B gives the parent class (see above); C gives one or more properties that distinguishes that class from all other related classes.
Definitions for brain regions
When defining a brain region, the definition should include:
- "Differentia" or what makes this brain region different from another brain region (Defining criteria)
- The smallest "classical anatomical reference" that the brain region is contained within (Is part of)
- Organism that it is observed in (Species)
We prefer that people add information in the fields specified in the form (field names in parentheses), but we will accept free text in the definition field containing the information above.
Neurolex provides the means to add a reference to each statement made in Neurolex. If you add a class or link two pages, you can add a reference, in the form of a Pub Med ID (PMID). When adding the PMID, you should just add the number and not any prefix. If you want to add more than one PMID, separate them by semi-colons.
What are some best practices for choosing the name of a new concept?
Names need to be unique. Although Neurolex will accept special characters, avoid them if possible. The comma is particularly problematic, as some fields accept multiple entries separated by commas.
Names for brain regions
Area name first, and if needed, the reference the area comes from, labelled with the name of the first author and the year in parentheses.
- ex: Area 10M of Ongur (2003)
What is NeuroNames?
NeuroNames is another name for the resource BrainInfo. This resource has a lot of information about brain regions, so we frequently link out to it. To find the NeuroNames ID for a brain region, simply use the search at the BrainInfo site to find the structure you are interested in. Once you click on one of the results that comes back to you, you'll go to a page with a URL like the following:
The NeuroNames ID is the number after "ID=" in the URL. If you put this number into a NeuroLex form when it is asked, it will link back to this page automatically.
How can I get a private page to play around with that won't affect the rest of the site?
- From the main page, click on the upper right hand corner link that says "log in / create account"
- Click the link where it says: Don't have a login? Create an account.
- Fill out the form, including the little word puzzle at the top that verifies you are a human :)
- Once you have created the account, click the same link again in the upper right to log in
- Once you are logged in, you should see several links in the upper right hand corner. One of them will have the user name that you have chosen (next a little icon of a person). Click your user name link.
- This is your private page. Any edits that you make here will not be visible to other users.
Why are there so many different types of brain parts?
There are many different ways to divide up the brain. Although Neurolex takes a structural approach, i.e., we haven't yet defined neural systems like the visual system, we are still left with gross anatomy, cytoarchitecture, chemoarchitecture and connectivity, to name a few. Neurolex is concerned with building formal vocabularies for information systems. We therefore have to make sure that we create our ontologies as cleanly as possible, without mixing up all of these different types of parts. However, we don't expect a naive user to navigate all of these complexities. We therefore set up a few different types of categories into which users can deposit their brain parts. We are still trying to determine whether this is a useful exercise or not, but so far it seems to be working. We have started a page where we document our current categories (http://neurolex.org/wiki/Brain_parts_organization).
How can I get a list of the recent new categories?
- Quick way: click here
- Advanced way: From the new pages special page, select 'all' from the Namespace pull-down. It will show you the new categories that have been added recently. You may also filter out modifications to pages as you'd see in the recent changes list. Adding a user name to the form will let you look at new categories that a particular user name has added.
How can I see what categories have changed in a specific period of time?
Click here to see an example of how to see all classes that have changed after a particular date
What should I include in the description of a resource?
Copy or write a description of the resource, which will enable the general neuroscience public to discern whether or not the resource is likely to have the information that the person is looking for. This can often be obtained by reading the "about us" section of the resource. The first 3 sentences should contain the description of the resource and what one can get from it. An example is: CCDB is a database that contains high resolution images of cells For more information try https://confluence.crbs.ucsd.edu/display/NIF/Curation+Workflow and https://confluence.crbs.ucsd.edu/display/NIF/Curation+Best+Practices
What is a DISCO Sitemap and how do I generate one?
A DISCO Sitemap or Resource Description file is a service provided by the DISCO protocol that keeps your NIF Registry description up-to-date and informs search engines about your resource. DISCO can ingest many formats, such as the native "disco.rd", the NIF "disco.rd.nif.rdf" and the National Center for Biomedical Computing's Biositemap formats. Resource owners may login (upper right) and find their resource. Under the “Are you the owner of this resource?” section, click on the [Clink here to generate sitemap] link and follow the instructions.
How do I add a brain region to Neurolex?
Neurolex provides a special extended form for brain regions that makes it easier to define the properties of brain regions and link to images. If you are adding a new brain region to Neurolex, the easiest way to invoke the form is to use the "Create a new brain region" box on the home page. This will automatically classify the brain region as "Regional part of brain" and bring up the extended form. If the brain region already exists in Neurolex, you should click "Edit with form". If this doesn't show the extended form, you have to use a few tricks. Click "Edit with form" use the following steps:
- 1) Replace the Supercategory with "Regional part of brain"
- 2) Scroll to the bottom and look at the Free text box
- 3) Delete any Category information, e.g., Regional part of thalamus
- 4) Copy and paste the following text: "Page has default form::PONS brain region| " (remove quotes and enclose in double brackets)
- 5) Save edits
- 6) Click "Refresh" on the top right menu, next to the Edit functions.
How do I reference NeuroLex content via URIs?
All entries within Neurolex can be accessed via their NeuroLex ID. This is achieved through the use of a standard URI mechanism. The format of the URIs is as follows:
The following examples are provided for the use of the base NeuroLex URI :
- Hippocampus CA1 pyramidal cell
What is the difference between and assay and a protocol?
Why does Neurolex have both Imaging assay and Imaging protocol? NIF has been loosely modeling its investigation-related content on the Ontology of Biomedical Investigation. Our current model (Feb 2013) separates Assays and Protocols according to their specification. An assay is a planned process designed to measure something, i.e., something that you intend to do, while the protocol is the plan specification, i.e., the steps you followed. Assay is an action, while protocol is an information entity. Assays are thus specified by protocols. We have created the Specified by property to connect the two, i.e., an Assay is specified by a protocol. We are moving towards removing the "assay" and replacing it with the action, e.g., imaging, as that is most commonly used.
Who can I contact with more questions?
Mailing list: neurolex at googlegroups.com
Maryann Martone: maryann at ncmir.ucsd.edu
Stephen Larson: slarson at ncmir.ucsd.edu