# Graph Oriented Objects for Ruby (Goo) *Goo* is a Ruby library that provides ORM-alike capabilities to interact with [RDF](http://en.wikipedia.org/wiki/Resource_Description_Framework)/[SPARQL](http://en.wikipedia.org/wiki/SPARQL) backends. *Goo* provides a DSL for defining schemas for objects and controls how they get validated, serialized, saved, and retrieved from the triplestore. Using RDF and SPARQL for large-scale applications creates challenges in terms of scalability and technology adoption. We designed Goo with two main objectives: * *Goo* abstracts SPARQL so developers do not need to be SPARQL experts to handle large RDF graphs efficiently. * *Goo* is designed to serve [BioPortal](http://bioportal.bioontology.org/) growing REST traffic. BioPortal's REST API provides access to hundreds of millions of Biomedical artifacts. Scalability and efficiency is at the core of *Goo's* design. :::info Source code see: ::: # How to use :::info Github documentation see: ::: ## Examples ### Example: getting a user and editing it Using bin/ncbo_cron --console ```ruby user = LinkedData::Models::User.find("admin").first user.bring_remaining user.password=("my_password") user.valid? user.save ``` ### Example: get all mappings ```ruby LinkedData::Models::Mappings.all.include(:id, :source, :classes) #Get all mappings with all attributes LinkedData::Models::RestBackupMapping.all .include(LinkedData::Models::RestBackupMapping.attributes(:all)).each do |m| puts m.id.to_s end #Get and delete all mappings LinkedData::Models::RestBackupMapping.all.each do |m| puts m.id.to_s mapping_id = RDF::URI.new(m.id.to_s) puts LinkedData::Mappings.delete_rest_mapping(mapping_id) end ``` ### Example: get a slice and edit it ```ruby # Retrieve an ontology ont = LinkedData::Models::Ontology.find("STY").first sub = ont = LinkedData::Models::Ontology.find("STY").include(LinkedData::Models::Ontology.attributes(:all)).first # Retrieve all submissions of ont sub = LinkedData::Models::OntologySubmission.where(ontology: ont).include(:submissionId).include(:submissionStatus).all # Retrieve a submission of ont1 including all its attributes sub = LinkedData::Models::OntologySubmission.where(ontology: ont).include(LinkedData::Models::OntologySubmission.attributes(:all)).first # Retrive latest submission and bring all properties sub = ont.latest_submission sub.bring_remaining sub.ontology.bring_remaining # Retrieve a slice slice = LinkedData::Models::Slice.find("umls").include(:acronym, :name, :ontologies).first # To include all attributes: slice = LinkedData::Models::Slice.find("umls") .include(LinkedData::Models::Slice.attributes(:all)) .first # Change the name slice.name = "test" # Change the ontologies of this slice slice.ontologies = [ont] # Save the changes if slice.valid? slice.save end # Display errors slice.errors ``` # How it works ## Model set up ### Model settings TODO see ### Model attributes ```ruby # Get all attributes of a model LinkedData::Models::OntologySubmission.attributes(:all) # Get the settings of an attribute LinkedData::Models::OntologySubmission.attribute_settings(:naturalLanguage) # Returns the following JSON object {:namespace=>:omv, :enforce=>[:list]} # Get the value of an attribute? # In OntologySubmission.rb self.naturalLanguage = "en" ``` ## Generating SPARQL queries There are 7 types of generated queries ### Include/unmapped/general query ```sql SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM # for each graph from 1..n WHERE { ?id a . OPTIONAL { { ?id ?attributeObject . BIND("var_1" as ?attributeProperty) } UNION .... UNION { ?attributeObject ?id . BIND( "var_j" as ?attributeProperty)} # if attribute_j_uri is an inverse attribute UNION .... { ?id ?attributeObject . BIND("var_n" as ?attributeProperty) } } FILTER(?id = ) } ``` ### Aggregate query TODO ### BNODE query ```sql SELECT DISTINCT ?id ?line1 ?line2 FROM WHERE { ?id a . ?id _:g64460 . _:g64460 ?line1. _:g64460 ?line2 . FILTER(?id = || ?id = ) } ``` ### FILTER query (`test/test_where#test_filter`) ```sql SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM WHERE { ?id a . ?id ?internal_join_var_0 . #can alos be optional FILTER(?internal_join_var_0 > "var") } ``` ### ORDER BY query ```sql SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM WHERE { ?id a . ?id ?internal_join_var_0 . #can also be optional } ORDER BY ?internal_join_var_0 ``` ### Equivalent predicates case see `def self*.expand_equivalent_predicates(query, eq_p)` ```sql SELECT DISTINCT ?id ?attributeProperty ?attributeObject FROM WHERE { ?id a . OPTIONAL { {?id ?attributeObject . BIND( "var_1" as ?attributeProperty)) } UNION ... UNION {?id ?attributeObject . BIND( "var_1" as ?attributeProperty)) } ... } ``` --- **Documents** - [💁‍♂️ Acknowledgments](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/acknowledgments-15GdRXLQdm) - [📚Publications and references](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/publications-and-references-87tEoeoGKy) - [🗽Terms & Conditions](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/terms-conditions-naDsDo2Zxq) - [🧞‍♂️Metadata guidelines and recommendations](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/metadata-guidelines-and-recommendations-pOFbK9sIfp) - [📜 AgroPortal Release Notes](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/agroportal-release-notes-btKjZk5tU2) - [ 👩‍🚀 User Guide](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/user-guide-ZszoBwfjGF) - [📎 API Documentation](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/api-documentation-kMCurGKD97) - [🤖 Developer Documentation](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/developer-documentation-LhsrucqGTa) - [🗃External Documentation](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/external-documentation-vNPQCdArrr) - [AgroPortal infrastructure](https://wiki.agroportal.eu/s/e6158eda-c109-4385-852c-51a42de9a412/doc/agroportal-infrastructure-ietsAU4kPs)