PD2AF is a tool intended for translation of SBGN maps from Process Description to Activity Flow language.
## Project Navigation
*[REPOSITORY](https://gitlab.com/pd2af/pd2af) with all the relevant project's data
*[WEB INTERFACE](http://188.166.159.222/translator.html) for converter
*[SBGN EXAMPLES](https://gitlab.com/pd2af/pd2af/tree/master/knowledge/sbgn-examples/metabolismregulation.org) from *Metabolism Regulation project*
*[ISSUES](https://gitlab.com/pd2af/pd2af/issues) with current bugs and planned features
*[CONVERTER RULES](https://gitlab.com/ddenniss/odysseus_modules/blob/master/pd2af/pd2af.rkt) implemented in Racket language
*[TRANSLATION ONTOLOGY](https://gitlab.com/pd2af/pd2af/tree/master/knowledge/sbgn_translation_ontology/sbgn_translation.tree) that describes terms and ideas, used in the converter's code
TranslationOntology a:Class subclass-of:Ontology d:"An ontology that maps SourceOntology into TargetOntology" comment:"I am not sure which name is more proper to use: Mapping Ontology or Translation Ontology"@author/ds
AllDifferent instance-of:rdfs/Class label:"AllDifferent" comment:"The class of collections of pairwise different individuals" subclass-of:rdfs/Resource
AllDisjointrdfs/Classes instance-of:rdfs/Class label:"AllDisjointrdfs/Classes" comment:"The class of collections of pairwise disjoint classes" subclass-of:rdfs/Resource
AllDisjointClasses instance-of:rdfs/Class label:"AllDisjointClasses" comment:"The class of collections of pairwise disjoint classes" subclass-of:rdfs/Resource
AllDisjointProperties instance-of:rdfs/Class label:"AllDisjointProperties" comment:"The class of collections of pairwise disjoint properties" subclass-of:rdfs/Resource
Annotation instance-of:rdfs/Class label:"Annotation" comment:"The class of annotated annotations for which the RDF serialization consists of an annotated subject, predicate and object" subclass-of:rdfs/Resource
AnnotationProperty instance-of:rdfs/Class label:"AnnotationProperty" comment:"The class of annotation properties" subclass-of:rdf/Property
regexp domain:Datatype range:Regexp d:"A regular expression that defines a range of possible symbols and their combinations for scalar datatypes"
Resource eq:rdfs/Resource
rel a:Property domain:Resource range:Resource d:"Establishes relation between Object and Subject"
same-as owl/sameAs:owl/sameAs
; TODO: at reading, semantic should be following: first read all properties from the class pointed by owl/sameAs, and then overwrite them by properties pointed directly in the definition line. In this case type owl/Property will be overwrited by type owl/SymmetricProperty
section-class a:Property domain:TabtreeSection range:Class d:"Defines default classes of the items in subsequent hierarchy" example:"For section 'classes' it would be 'section-class:Class', for section 'properties' it would be 'section-class:Property'"
section-hierarchy-relation a:Property domain:TabtreeSection range:Property d:"Defines relations between elements in subsequent hierarchy that follows current section in .tree file. Relation goes from one element (subject) to another element (object), that is always exactly one level up in hierarchy"
ICLondon name:"Imperial College London" hq:London start:1823
ISanger hq:Hinxton
MIB name:"Manchester Institute of Biotechnology" hq:Manchester uni:UManchester start:2006 url:mib.ac.uk
MCISB name:"Manchester Centre for Integrative Systems Biology" uni:UManchester
OUCS deabbr:"Oxford University Computing Services" hq:Oxford uni:UOxford start:1958 end:2012
france
ANL name:"Argonne National Laboratory" hq:Lemont start:1911
EISBM name:"European Institute for Systems Biology and Medicine" hq:Lyon
ENPC name:"École nationale des ponts et chaussées" hq:Champs-sur-Marne start:1747
ICurie name:"Curie Institute" hq:Paris
INRIA name:"French Institute for Research in Computer Science and Automation" hq:Rocquencourt office:Bordeaux,Grenoble,Lille,Nancy,Rocquencourt,Rennes,Saclay,Sophia_Antipolis start:1967
germany
ARI name:"Aerodynamic Research Institute" hq:Gottingen
CBioTu deabbr:"Center for Bioinformatics Tubingen" uni:UTubingen
FZI/AIFB name:"Research Center for Information Technology" hq:Karlsruhe uni:KIT url:fzi.de
HITS name:"Heidelberg Institute for Theoretical Studies" hq:Heidelberg start:2010 url:h-its.org
IMISE deabbr:"Institute for Medical Informatics, Statistics and Epidemiology" uni:ULeipzig
SPIIRAS name:"Санкт-Петербургский институт информатики и автоматизации" hq:Saint-Petersburg start:1977
VINITI alt-id:ВИНИТИ_РАН name:"Всероссийский институт научной и технической информации РАН" hq:Moscow start:1952 url:viniti.ru d:"maintains the largest publications database in Russia"
