@@ -82,7 +79,7 @@ You can access it through the 'Add On' menu option.
### Ontology Search
-From OntoMaton, you can search three different services within one tool: the [NCBO Bioportal](http://bioportal.bioontology.org/), [Linked Open Vocabularies](http://lov.okfn.org) and [EBI Ontology Lookup Service](https://www.ebi.ac.uk/ols/), and insert the terms in your Google Spreadsheet directly. Full term provenance is recorded for you and later downstream analysis.
+From OntoMaton, you can search three different services within one tool: the [NCBO Bioportal](http://bioportal.bioontology.org/), [Linked Open Vocabularies](https://lov.linkeddata.es) and [EBI Ontology Lookup Service](https://www.ebi.ac.uk/ols/), and insert the terms in your Google Spreadsheet directly. Full term provenance is recorded for you and later downstream analysis.
@@ -90,7 +87,7 @@ From OntoMaton, you can search three different services within one tool: the [NC
### Ontology Tagging
-With OntoMaton, you can select a number of spreadsheet cells and then 'tag' them. This means that OntoMaton will take the terms in the cells and send them to BioPortal's Annotator service. The results will come back as a list of the free text terms, showing for each all matches in BioPortal.
+With OntoMaton, you can select a number of spreadsheet cells and then 'tag' them. This means that OntoMaton will take the terms in the cells and send them to BioPortal's Annotator service. The results will come back as a list of the free text terms, showing for each all matches in BioPortal.
@@ -98,16 +95,14 @@ With OntoMaton, you can select a number of spreadsheet cells and then 'tag' them
### Configuring OntoMaton - Settings
-
From the settings screen, you can configure:
-* How terms should be inserted in to the spreadsheet when not in 'ISA mode' (where the next columns aren't named 'Term Source REF' or 'Term Source Accession'). The two options are as either as a hyperlink to the term in Bioportal/OLS/LOV or as a term name with the hyperlink in parentheses.
-* Restrictions, which specify for zero or more columns (with a name in the first cell), restrictions that should be placed on the search space per each of the ontology lookup services we use (Bioportal/OLS/LOV) E.g. the column 'Label' is restricted to terms from the Chemincal Entities of Biomedical Interest ontology (ChEBI). Please, note that for instance if a column has a restriction over the BioPortal service, the restiction will not have an effect if searching terms with OLS.
-
+- How terms should be inserted in to the spreadsheet when not in 'ISA mode' (where the next columns aren't named 'Term Source REF' or 'Term Source Accession'). The two options are as either as a hyperlink to the term in Bioportal/OLS/LOV or as a term name with the hyperlink in parentheses.
+- Restrictions, which specify for zero or more columns (with a name in the first cell), restrictions that should be placed on the search space per each of the ontology lookup services we use (Bioportal/OLS/LOV) E.g. the column 'Label' is restricted to terms from the Chemincal Entities of Biomedical Interest ontology (ChEBI). Please, note that for instance if a column has a restriction over the BioPortal service, the restiction will not have an effect if searching terms with OLS.
### Restricting OntoMaton's search space
@@ -119,19 +114,17 @@ From the settings screen, you can configure:
-
When you add a restriction using the 'Settings' panel for the first time, a 'Restrictions' sheet will be added automatically. This sheet will have the following column headers:
-```Column Name | Ontology | Branch | Version | Ontology Name | Service```. Then you may define for a particular column header in your spreadsheet what ontology should be searched (or list of ontologies) over what service (BioPortal, OLS or LOV). A restriction will only apply if using the corresponding service for search.
+`Column Name | Ontology | Branch | Version | Ontology Name | Service`. Then you may define for a particular column header in your spreadsheet what ontology should be searched (or list of ontologies) over what service (BioPortal, OLS or LOV). A restriction will only apply if using the corresponding service for search.
Additionally, within one ontology restriction, for BioPortal searches, you can restrict to a particular branch of an ontology, providing a way to further restrict the search space.
An example of a google spreadsheet with such functionality can be viewed here: https://docs.google.com/spreadsheet/ccc?key=0Al5WvYyk0zzmdDNLeEcxWHZJX042dS0taXJPNXpJMHc
-
### Video Tutorial
Access the video tutorial showing how to install and use OntoMaton (version 1) [here](http://www.youtube.com/watch?v=Qs0nxGBfQac&feature=player_embedded).
-
+
### Templates
Templates can be found through accessing them on the google templates site. OntoMaton templates are [here](https://drive.google.com/templates?type=spreadsheets&q=ontomaton).
@@ -149,5 +142,3 @@ This work is licensed through a [CPAL license](http://isatab.sf.net/licenses/Ont
### Merchandise
Fancy an OntoMaton t-shirt? We haven't got any to give away...yet! But...you can buy one of these rather snazzy t-shirts from [Spreadshirts](http://antarctic-design.spreadshirt.co.uk/men-s-classic-t-shirt-A22910590/customize/color/2) for just £15!
-
-
diff --git a/Settings.gs b/Settings.gs
index 1454bc9..15b2ced 100644
--- a/Settings.gs
+++ b/Settings.gs
@@ -147,7 +147,7 @@ function getBioPortalOntologies() {
function getLinkedOpenVocabularies(){
- var vocabsURL = "http://lov.okfn.org/dataset/lov/api/v2/vocabulary/list";
+ var vocabsURL = "https://lov.linkeddata.es/dataset/lov/api/v2/vocabulary/list";
var cache = CacheService.getPrivateCache();
if (cache.get("lov_fragments") == null) {
-2. Click on 'Get add-ons...' and then search for 'OntoMaton':
+2. Click on 'Get add-ons...' and then search for 'OntoMaton':
@@ -67,8 +65,7 @@ Here you can click on the image and read more about OntoMaton:
@@ -82,7 +79,7 @@ You can access it through the 'Add On' menu option.
### Ontology Search
-From OntoMaton, you can search three different services within one tool: the [NCBO Bioportal](http://bioportal.bioontology.org/), [Linked Open Vocabularies](http://lov.okfn.org) and [EBI Ontology Lookup Service](https://www.ebi.ac.uk/ols/), and insert the terms in your Google Spreadsheet directly. Full term provenance is recorded for you and later downstream analysis.
+From OntoMaton, you can search three different services within one tool: the [NCBO Bioportal](http://bioportal.bioontology.org/), [Linked Open Vocabularies](https://lov.linkeddata.es) and [EBI Ontology Lookup Service](https://www.ebi.ac.uk/ols/), and insert the terms in your Google Spreadsheet directly. Full term provenance is recorded for you and later downstream analysis.