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'''7) How are categories related to one another in NeuroLex?
'''7) How are categories related to one another in NeuroLex?
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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" relatiionship, 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";  "Has location";  "Has 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]].
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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" [[Category:Neuron | Neuron]].  In order to make sure that each Category is related to its parent only through an "is a" relatiionship, 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";  "Has location";  "Has 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]].
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Revision as of 16:56, 20 February 2009

1) 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 and not in providing general information about the concept. It is a dictionary rather than an encyclopedia. We want to make explicit the way in which a concept is defined so that it can be consistently applied to data annotation. 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.

2) How will the NeuroLex be used?

The NeuroLex will provide a resource for those annotating data or developing methods to search and integrate data based on the meaning of concepts. For the Neuroscience Information Framework project, the NeuroLex will provide the base set of concepts from which we are developing the NIFSTD ontologies. We hope that other groups will also use these base concepts to build their information resources. By using the same core concepts, we can easily connect these different resources together.

3) 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.

4) 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.

5) 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.

6) 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

7) 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". In order to make sure that each Category is related to its parent only through an "is a" relatiionship, 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"; "Has location"; "Has 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.




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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.