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@@ -1,4 +1,61 @@
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-Creating Content
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-=================
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+Creating Content Types
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+======================
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-Lorem ipsum
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+ Tripal v3 comes with some pre-defined content types, however you have the ability to create new Content Types through the Administrative user interface! In Tripal v3, all content types are defined by public ontology terms. This has a number of advantages:
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+
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+1. Facilitates sharing between Tripal sites,
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+2. Provides a clear indication of what content is available in your site,
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+3. Makes content creation more intuitive (add a "Gene" rather then a "feature")
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+4. Allows complete customization of what data types your site provides
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+5. Integrates tightly with web services allowing Tripal to adhere to RDF specifications
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+
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+Find an Ontology Term
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+---------------------
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+This is likely the most difficult step as it seems ontologies are both plentiful and sparse at the same time. We highly recommend discussing your content with the community so that the same term can be used across Tripal sites for the same data. If your data is genomics based, you need look no further than the sequence ontology. The following table lists some recommended terms for common genomic data:
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+
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+.. csv-table::
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+ :header: "Term Name", "Accession", "Examples", "Comments"
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+
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+ "genome", "SO:0001026", "specific genome assembly", "*See the note below about genome assemblies.*"
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+ "chromosome", "SO:0000340", "", "Think carefully about whether it's useful to provide pages for chromosomes. The typical fields provided for content stored in the Chado feature table such as relationship and sequence listing can cause long page loads for not very useful information. Thus if you are going to provide pages you might want to include more summary fields based on materialized views to provide more useful content to users."
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+ "supercontig", "SO:0000148", "", "This term is a synonym for scaffold and should be used for such"
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+ "contig", "SO:0000149", "", ""
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+ "gene", "SO:0000704", "", ""
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+ "mRNA", "SO:0000234", "", ""
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+ "sequence_variant", "SO:0001060", "SNP, MNP, Indel", "We recommend grouping all variants into a single content type in order to provide a common page layout across variant types and to make searching across variants (e.g. show me all variants in a given region) easier. This also makes it easier to support new variant types in the future."
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+ "genetic_marker", "SO:0001645", "KASP, Exome Capture, GBS", "We recommend grouping all genetic markers for the same reasons we recommend grouping all sequence variants. You can then specify the type of variant or marker in the featureprop table."
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+
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+.. note::
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+
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+ There are a few ways you might choose to store genome assemblies in Chado:
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+
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+ 1. The analysis table. Chromosomes or scaffolds are linked via the analysisfeature table. This is the method Tripal uses by default.
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+ 2. The feature table. Chromosomes or scaffolds are also stored in the feature table and linked to the genome feature via the feature_relationship table.
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+ 3. The project table. Chromosomes or scaffolds are stored in the feature table and linked using the project_feature table.
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+ There is discussion in the community about which of these three is the best method.
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+
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+For non-genomic data, it can be challenging to find an appropriate term for your content type as both the number and maturity of ontologies is decreased. However, a good starting place is `EBI's Ontology Lookup Service <http://www.ebi.ac.uk/ols/index>`_. At this site you can search for terms that may match your content type. You may find a perfect term, but if you are uncertain if a term is appropriate please open an issue on `Tripal's GitHub project page <https://github.com/tripal/tripal/issues>`_ to encourage discussion among the community for the ideal term. Not only will this provide you with help and input in your own search for an ontology term, it will also help others with similar data. We intend to add to this page once decisions are made for other data types to make this process easier and encourage sharing of data between Tripal sites. If all else fails and you can not find an appropriate existing term, it is possible to create a **local* term within the **local** vocabulary. In this case describe your term carefully, add it to the database, and use it for content creation.
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+
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+Add the Vocabulary Term
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+Once you've choosen a term to describe your content type, you should add the term to Tripal. If the term belongs to a controlled vocabulary with an file in OBO format then you can load all the terms of the vocabulary using Tripal's OBO Loader at Tripal → Data Loaders → Chado OBO Loader. See the Controlled Vocabularies section of the tutorial for more details. For adding a single term either from an existing vocabulary or a new local term, navigate to Tripal → Data Loaders → Chado Controlled Vocabularies and search to see if the vocabulary already exists. If it does you do not need to add the vocabulary. If it does not exist, click the Add Vocabulary link to add the vocabulary for your term. Then navigate to Tripal → Data Loaders → Chado CV Terms then click the Add Term link to add the term.
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+
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+Create a Tripal Content Type
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+Start by navigating to Structure → Tripal Content Types and then click on the Add Tripal Content Type link at the top. This will take you to a form that leads you through the process of creating a custom Tripal Content Type. First, enter for the name of the term you would like to use to describe your content in the Content Type autocomplete textbox (e.g. genetic_marker). This term cannot be changed later so make sure you put a lot of thought into it in the previous step. Then click Lookup Term. This should bring up a list of matching terms from which you can select the specific term you would like to use.
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+
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+
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+It will also bring up a section to specify which Chado tables you want the data for this content type stored in. Since genetic markers are sequence features, we would like to store them in the chado feature table. One you select the Chado table, the form will update with a number of leading questions to determine how to tell which records in a chado table belong to a given content type. Specifically, the following options are supported if the appropriate fields/tables are available:
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+
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+All records in the table belong to the current content type (e.g. organism)
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+Records in the table where the type_id matches the content type term belong to the content type (e.g. genetic_marker)
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+Records in the primary table that have a specific property stored in an associated *prop table (e.g. Genotyping Projects)
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+Records in the primary table that have a specific annotated term in an associated *_cvterm table
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+For genetic markers, we can simply use the type_id to differentiate which records in the feature table are genetic markers. Thus we
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+
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+Select "No" not all records in the feature table are genetic markers
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+Type Column: type_id
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+Then click Create Content Type to create a custom genetic marker content type.
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+
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+
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+
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+Once you create a custom content type, you can create pages of that type for your users either through the create tripal content user interface as we did for organisms or by loading your data into chado and then publishing it like we did for genes and mRNAs.
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Stephen Ficklin