Adding ability to load individuals from in-memory data as well as off-disk.

[julesjacobsen]

Fix for @drseb in issue #57 enabling individuals data to be loaded into the knowledgebase from a Map rather than off disk.

[julesjacobsen]

One question on naming. Should .loadDataFromMap(data) really be loadIndividuals? We still have no way of importing labels and presumably this requires different OWLAPI calls.

[cmungall]

individualAssociations would be more precise We need the label loading to get human-friendly results returned. Some clients will have their own way of doing a lookup, others will rely on the service ``` addAxiom(df.getOWLAnnotationAssertionAxiom(df.getRDFSLabel(), ind.getIRI(), df.getOWLLiteral(label)) ```

[julesjacobsen]

OK so these methods need to change their signatures too. Here 'data' means 'individualAssociations'. Does this make sense for loadDataFromOntology be changed to loadIndividualAssociationsFromOntology given these are actually just being merged? Should there just be a single set of loadOntology or loadInstancedOntology?

         public Loader loadDataFromOntology(String path) {
            sourceDataBuilder.dataOntology(path);
            return this;
        }

        public Loader loadDataFromOntologies(String... paths) {
            sourceDataBuilder.dataOntologies(paths);
            return this;
        }

        public Loader loadDataFromOntologies(Collection<String> paths) {
            sourceDataBuilder.dataOntologies(paths);
            return this;
        }

        public Loader loadDataFromTsv(String path) {
            sourceDataBuilder.dataTsv(path);
            return this;
        }

        public Loader loadDataFromTsv(String... paths) {
            sourceDataBuilder.dataTsv(paths);
            return this;
        }

        public Loader loadDataFromTsv(Collection<String> paths) {
            sourceDataBuilder.dataTsv(paths);
            return this;
        }

        public Loader loadDataFromMap(Map<String, ? extends Collection<String>> data) {
            sourceDataBuilder.data(data);
            return this;
       }

[julesjacobsen]

@cmungall / @jnguyenx can you comment on this further or merge this please. We can add the labels in another PR.

[cmungall]

I haven't had time to fully explore but broadly this looks good

[drseb]

We should now have a thought about how to add additional information to an annotation. E.g. a weight or something.

Is it already possible to add negation?

[drseb]

I think it is good. Thanks. Can't test this right now.

[julesjacobsen]

OK, cheers for looking. @drseb I think this should make it possible to do what you need. If not, open another ticket.

[drseb]

Thanks. I will test ASAP

[jnguyenx]

Looks good to me!