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Chado data loaders and other tools

Java 14.07% Shell 0.10% Perl 60.76% Makefile 0.09% PLpgSQL 1.44% XSLT 1.06% HTML 2.59% Perl 6 18.11% CSS 0.08% Python 0.17% PHP 0.67% TSQL 0.86%

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seperate chado tools from chado schema

see: GMOD/Chado#79

to generate this repo, i cloned the chado repo, changed the origin to this one, and then ran:

git filter-branch --index-filter "git rm -rf --cached --ignore-unmatch chado/modules" --prune-empty
git filter-branch --index-filter "git rm -r --cached --ignore-unmatch chado/schemas" --prune-empty -f

which purges the chado/schemas and chado/modules directories from the history.

gmod_load_cvterms.pl does not (yet) support cross cv relationships

Original issue posted by @bellerbrock

Attempting to load related crop ontology terms in separate namespaces (e.g. "YamTrait" and "YamVariable") results in the error "Cross referencing relationships across namespaces is not supported (yet.. ) SKIPPING this relationship!".

So far, the way we get around this error is to load everything in a single namespace, but then we end up with mixed ontologies. Could we update the loading script to support cross referencing? The big advantage is that it would let us load more refined namespaces, which in turn would make it easy to distinguish which terms can have phenotype measurements linked to them, and how terms can be used for trait composing.

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