Add get methods for *sets

getReadGroupSet, getCallSet and getDataset
Allow searching for references by refSetId
Add variantSet.referenceSetId field
Declare properPlacement == SAM flag 0x2
Using a GAOntologyTerm for cell type rather than a string.
Using OntologyTerm rather than string from Cell Line

Note there may not be consensus on this. There are competitors in this
space, but the general schema should support any
Added link to Uberon
Added documentation for making an OntologyTerm for a taxon
making links markdown-friendly
making links (CL, CLO) markdown-friendly
removing obsolete GA prefix. See comments from @mbaudis on issue #164
Merge pull request #164 from cmungall/ontology

Use of ontologyTerm for cell types and cell lines
Merge pull request #180 from cassiedoll/methods

Add get methods for *sets
Merge pull request #182 from cassiedoll/variant-ref

Add variantSet.referenceSetId field
Merge pull request #181 from cassiedoll/refset

Allow searching for references by refSetId
Merge pull request #183 from cassiedoll/properplacement

Declare properPlacement == SAM flag 0x2