diff --git a/docs/building/002_species_functional_data.md b/docs/building/002_species_functional_data.md index ffa2025..ba1204a 100644 --- a/docs/building/002_species_functional_data.md +++ b/docs/building/002_species_functional_data.md @@ -60,7 +60,7 @@ Gene2 GO:0000227 ISS ... ``` -On the 'Admin panel', under 'Add' -> 'GO Genes' such a file can be +In the 'Admin panel', under 'Add' -> 'GO Genes' such a file can be uploaded, for a species. Additionally a description needs to be provided from where the GO terms in the file originate from (the source). @@ -69,4 +69,26 @@ from where the GO terms in the file originate from (the source). **InterPro** domains can be imported directly from [InterProScan](http://www.ebi.ac.uk/interpro/download.html) output. To do so, in the 'Admin panel', under 'Add' -> 'InterPro genes' select a species, select the file and click 'Add InterPro' -![InterPro gene](../images/add_interpro_gene.png "Adding InterPro terms for a species") \ No newline at end of file +![InterPro gene](../images/add_interpro_gene.png "Adding InterPro terms for a species") + +## Adding external references and aliases/tokens + +Some genes have an short handle that is easier to remember, this is also called the alias, +gene symbol or token. CoNekT uses these short labels in network graphs when they are +available. In addition to this, external references can be added to genes connecting your +release with existing platforms. + +In the 'Admin panel', under 'Add' -> XRefs Genes this can be done. Select the **species** +first, and as platform select **custom**. Select a file containing the xrefs, here a +tab-delimited file is required with four columns, the gene ID in CoNekT, the gene ID or token, +the name of the external platform or 'token' in case it is a symbol/alias/token, and a url +(empty in case no link exists). + +``` +Gene1 GN01 token +Gene1 alternative_name token +Gene1 gene1 other_db http://www.other-db.com/view/gene/gene1 +... +``` + +![xrefs gene](../images/add_xrefs_genes.png "Adding XRefs to genes") \ No newline at end of file diff --git a/docs/building/004_coexpression_network_cluster.md b/docs/building/004_coexpression_network_cluster.md new file mode 100644 index 0000000..9299c51 --- /dev/null +++ b/docs/building/004_coexpression_network_cluster.md @@ -0,0 +1,7 @@ +#### Adding coexpression network + +*UNDER CONSTRUCTION* + +#### Adding coexpression clusters + +*UNDER CONSTRUCTION* \ No newline at end of file diff --git a/docs/building/005_comparative_genomics.md b/docs/building/005_comparative_genomics.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/building/006_precomputing_counts_etc.md b/docs/building/006_precomputing_counts_etc.md new file mode 100644 index 0000000..161cbc9 --- /dev/null +++ b/docs/building/006_precomputing_counts_etc.md @@ -0,0 +1,3 @@ +# Computing enrichments, similarities, and counts ... + +*UNDER CONSTRUCTION* \ No newline at end of file diff --git a/docs/building_conekt.md b/docs/building_conekt.md index eb168c5..f5b4b1b 100644 --- a/docs/building_conekt.md +++ b/docs/building_conekt.md @@ -24,22 +24,7 @@ Step-by-step instructions * [Adding GO term and InterPro domain definitions](./building/001_GO_InterPro_domains.md) * [Adding a new species and functional data](./building/002_species_functional_data.md) * [Adding expression profiles](./building/003_expression_profiles.md) + * [Adding co-expession networks and clusters](./building/004_coexpression_network_cluster.md) + * [Adding comparative genomics data](./building/005_comparative_genomics.md) + * [Precomputing counts and more](./building/006_precomputing_counts_etc.md) - - - -#### Adding coexpression network - -*UNDER CONSTRUCTION* - -#### Adding coexpression clusters - -*UNDER CONSTRUCTION* - -### Adding external references - -*UNDER CONSTRUCTION* - -### Computing enrichments, similarities, and counts ... - -*UNDER CONSTRUCTION* \ No newline at end of file diff --git a/docs/images/add_expression_profiles.png b/docs/images/add_expression_profiles.png index 87b945c..8e312de 100644 Binary files a/docs/images/add_expression_profiles.png and b/docs/images/add_expression_profiles.png differ diff --git a/docs/images/add_functional_data.png b/docs/images/add_functional_data.png index 488c1fb..3193c8b 100644 Binary files a/docs/images/add_functional_data.png and b/docs/images/add_functional_data.png differ diff --git a/docs/images/add_go_gene.png b/docs/images/add_go_gene.png index 923e159..45bc5ed 100644 Binary files a/docs/images/add_go_gene.png and b/docs/images/add_go_gene.png differ diff --git a/docs/images/add_interpro_gene.png b/docs/images/add_interpro_gene.png index 04933e0..9c1331f 100644 Binary files a/docs/images/add_interpro_gene.png and b/docs/images/add_interpro_gene.png differ diff --git a/docs/images/add_species.png b/docs/images/add_species.png index da2b8f1..151c6ef 100644 Binary files a/docs/images/add_species.png and b/docs/images/add_species.png differ diff --git a/docs/images/admin_home.png b/docs/images/admin_home.png index 525c61b..c588ab1 100644 Binary files a/docs/images/admin_home.png and b/docs/images/admin_home.png differ