diff --git a/misc-scripts/ontology/README b/misc-scripts/ontology/README
deleted file mode 100644
index a67643f9cba4fd7f7171771286081679a902def2..0000000000000000000000000000000000000000
--- a/misc-scripts/ontology/README
+++ /dev/null
@@ -1,288 +0,0 @@
- THE ENSEMBL ONTOLOGY DATABASE
- ====================================================================
-
- MOTIVATION
- --------------------------------------------------------------------
-
- Starting with release 55 of Ensembl we provide an ontology database
- called ensembl_ontology_NN (where 'NN' is the number of the
- release). It replaces the older ensembl_go_NN database which used
- to be loaded straight from the public table dumps provided by the
- Gene Ontology group (and hence weren't really an Ensembl database to
- start with). The older ensembl_go_NN database also had an external
- Perl API associated with it which often made working with GO terms
- in Ensembl slightly awkward, or at least more cumbersome than what
- it needed to be.
-
- The new database, and its associated native Ensembl Core API, is an
- attempt to make it easy to work with ontology terms in Ensembl.
-
- The database also contains Sequence Ontology (SO) terms even though
- these are not yet cross-referenced or otherwise used by Ensembl.
-
-
- THE DATABASE SCHEMA
- --------------------------------------------------------------------
-
- The ensembl_ontology_NN database consist of eight tables and a
- number of auxiliary tables.
-
- - ontology
- The 'ontology' table contains one entry for each "namespace",
- that is, for what the Gene Ontology group calls "ontology" and
- which is called "namespace" in OBO files. For GO this boils
- down to entries for 'molecular_function', 'cellular_component',
- and 'biological_process', and for SO this is a single 'sequence'
- entry.
-
- The fields are 'name' (either "GO" or "SO" for now) and
- 'namespace'. The function of this table is to separate ontology
- terms belonging to different ontologies and/or namespaces.
-
- - subset
- The 'subset' table contains information about each of the subsets
- of the loaded ontologies. GO subsets includes, for example,
- GOSlim GOA ('goslim_goa').
-
- - term
- The 'term' table contains the ontology term accession, name,
- and definition as well as a reference to its namespace in the
- 'ontology' table and the set of subsets that it belongs to within
- that ontology (if any).
-
- - synonym
- This table contains all synonyms that a term has.
-
- - relation_type
- The 'relation_type' table simply contains the different types
- of relationships that are defined between the ontology terms.
-
- For GO, the relationship types are currently 'is_a', 'part_of',
- 'regulates', 'positively_regulates', and 'negatively_regulates'.
-
- For SO, the relationship types are currently 'is_a',
- 'adjacent_to', 'derives_from', 'has_part', 'member_of',
- 'non_functional_homolog_of', 'part_of', 'position_of',
- 'sequence_of', and 'variant_of'.
-
- - relation
- The 'relation' table ties together the 'relation_type' table with
- the 'term' table. Each entry consists of reference to a child
- term, to a parent term, and to a relation type.
-
- There should not exist any relation between two terms belonging to
- different namespaces.
-
- - closure
- The 'closure' table contains the transitive closure over a
- selection of transitive relation types. The transitive relation
- types currently covered are 'is_a', 'part_of'.
-
- Each entry in the 'closure' table consists of a reference to a
- child term, to one of its ancestor terms ("parent"), a reference
- to an immediate child of the ancestor, called the sub-parent,
- and the distance between the child and the ancestor through the
- sub-parent (see figure below).
-
- [parent]
- |
- +--------------------------+
- | |
- [subparent] [other children of parent term]
- | |
- : +---------------+
- : :
- [other terms in the hierarchy]
- :
- :
- |
- [child]
-
- This table is computed by a Perl program (see below) from the
- 'relation' table and allows for quick retrieval of all ancestors
- of a particular ontology term, or of all its descendants.
-
- - meta
- The 'meta' table holds meta information about the data in the
- database, such as the time-stamp from the OBO files that were
- loaded into it and when the load into the database happened.
-
- - aux_XX_YY_map
- The various tables named 'aux_XX_YY_map', e.g.,
- 'aux_GO_goslim_goa_map' and 'aux_SO_SOFA_map', are simple mapping
- tables that maps term IDs from the 'XX' ontology ("GO" or "SO") to
- the term(s) in the 'YY' subset.
-
- The mapping tables are created using the information stored in the
- 'closure' table, and therefore it will be based on the 'is_a' and
- 'part_of' relationships.
-
-
- SCOPE OF API IMPLEMENTATION
- --------------------------------------------------------------------
-
- The aim of the re-design of the way ontology terms are used with
- Ensembl is not to provide a generic API for ontology terms but
- instead to provide the ability to use ontology terms in straight
- forward querying for standard Ensembl objects such as genes,
- transcripts, and translations. Hence, the API will treat the
- ontology database as read-only.
-
- The operations available on the ontology terms themselves are
- restricted to querying them for their basic attributes such as
- the term accession, name, and definition, as well as relational
- information such as their immediate parent and/or child terms.
- For a selection of transitive relationship types (currently the
- relation types 'is_a' and 'part_of') we also provide fast access
- to the set of all parent and/or child terms of any given term.
-
- The connection between the ontology terms and the genes,
- transcripts, and translations of Ensembl is currently based on GO
- term cross-references (Xrefs). We do not yet cross-reference SO
- terms to any of these object types.
-
-
- SUPPORTED OPERATIONS
- --------------------------------------------------------------------
-
- The ontology term adaptor, Bio::EnsEMBL::DBSQL::OntologyTermAdaptor,
- supports the following operations:
-
- 1. Fetching one ontology term from the database
-
- 1.a by accession
- $adaptor->fetch_by_accession($accession)
-
- 1.b by internal ID
- $adaptor->fetch_by_dbID($dbID)
-
- 1.c by name or synonym
- $adaptor->fetch_all_by_name($synonym, $ontology)
-
- 2. Fetching a set of terms from the database
-
- 2.a by name or synonym pattern (e.g. "%splice_site%")
- $adaptor->fetch_all_by_name($pattern)
-
- 2.b by a collection of internal IDs
- $adaptor->fetch_all_by_dbID_list(\@dbIDs)
-
- 2.c by their (immediate) parent term
- $adaptor->fetch_all_by_parent_term($term)
-
- 2.d by their (immediate) child term
- $adaptor->fetch_all_by_child_term($term)
-
- 2.e by an ancestor term
- $adaptor->fetch_all_by_ancestor_term($term)
-
- 2.f by a descendant term
- $adaptor->fetch_all_by_descendant_term($term)
-
- 3. Fetching a structure that encodes the ancestor relationships of
- a term.
- $adaptor->_fetch_ancestor_chart($term)
-
- Given an ontology term, which is a Bio::EnsEMBL::OntologyTerm
- object, some operations from the second set of operations above are
- also available on the object itself (2.b--2.e):
-
- 4. Fetching a set of terms from the database
-
- 4.a by their (immediate) parent term
- $term->children()
-
- 4.b by their (immediate) child term
- $term->parents()
-
- 4.c by an ancestor term
- $term->descendants()
-
- 4.d by a descendant term
- $term->ancestors()
-
-
- ADDITIONS TO THE EXISTING ENSEMBL CORE API
- --------------------------------------------------------------------
-
- To enable to use ontology terms in querying for Ensembl objects,
- two methods were added to GeneAdaptor, TranscriptAdaptor, and to
- TranslationAdaptor:
-
- - fetch_all_by_GOTerm()
-
- - fetch_all_by_GOTerm_accession()
-
- Given a GO term object, the fetch_all_by_GOTerm() method uses
- the DBEntryAdaptor to fetch objects that are cross-referenced
- with the GO term or with any of its descendants. The
- fetch_all_by_GOTerm_accession() method works similarly, but
- instead of a GO term object it takes a GO term accession.
-
-
- COMPLETE EXAMPLE PROGRAMS
- --------------------------------------------------------------------
-
- See the Perl programs 'scripts/demo1.pl' and 'scripts/demo2.pl'.
-
-
- CREATING THE ONTOLOGY DATABASE
- --------------------------------------------------------------------
-
- To create the ensembl_ontology_NN database for a release, the
- following steps needs to be followed:
-
- 1. Create the empty database by doing "CREATE DATABASE
- ensembl_ontology_NN" (where 'NN' is the current release) on ens-staging1.
-
- 2. Load the schema from 'tables.sql' located in
- ensembl/misc-scripts/ontology/sql/
-
- 3. Update the url for SO.obo file in script 'get_OBO_files.ksh' to the latest
- released version, if the version is not already up to date.
- Check directory: http://sourceforge.net/projects/song/files/Sequence%20Ontology/
- for available releases of the SO.obo file.
-
- 3. Run script 'get_OBO_files.ksh' to download all the currently
- handled ontologies.
- perl get_OBO_files.ksh
-
- 4. As a prerequisite to the next step, you'll need to install
- ONTO-PERL modules from:
- http://search.cpan.org/CPAN/authors/id/E/EA/EASR/ONTO-PERL/ONTO-PERL-1.31.tar.gz
- or use the version installed in: /software/perl-5.8.8/lib/site_perl/5.8.8
- and add the path where the module is installed to your perl path
-
- 5. Load the data from each downloaded ontology (curently we download GO, SO and EFO)
- file into the database using the script 'load_OBO_file.pl' (run the script without arguments
- for help on usage, it is simple). The script lives in
- ensembl/misc-scripts/ontology/scripts/
-
- e.g.: perl load_OBO_file.pl -h ens-staging1 -u ensadmin -p xxx -d ensembl_ontology_67 -f GO.obo -o GO
-
-
- 6. Delete the 'UNKNOWN' ontology row from the ontology table.
- Once you're finished loading all the ontology files run the load_OBO_file.pl script
- with option -delete_unknown:
- e.g.: perl load_OBO_file.pl -h ens-staging1 -u ensadmin -p xxx -d ensembl_ontology_67 -delete_unknown
-
- The script will delete the dummy ontology if none of the loaded terms are still linked to it.
- It will report a problem in case it finds any terms linked to the UNKNOWN ontology.
- This may indicate that you haven't loaded all the files as definitions for some terms are missing.
-
- 7. Compute the transitive closure (the 'closure' table in the
- database) by running the 'compute_closure.pl' in almost the same
- way as in step 4. This step may take some time.
-
- e.g.: perl compute_closure.pl -h ens-staging1 -u ensadmin -p xxx -d ensembl_ontology_67
-
- 8. Add the auxiliary map tables by running 'add_subset_maps.pl'
- with the same arguments that you used for the script in the
- previous step.
-
- e.g.: perl add_subset_maps.pl -h ens-staging1 -u ensadmin -p xxx -d ensembl_ontology_67
-
- 9. Copy the newly created database to ens-staging2 using ensembl/misc-srcipts/CopyDBOverServer.pl script.
-
-
-$Id$