<commit_before><?xml version="1.0"?>
<model name="genomic" package="org.intermine.model.bio">

  <class name="Author" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <collection name="publications" referenced-type="Publication" reverse-reference="authors"/>
  </class>

  <class name="BioEntity" is-interface="true">
    <attribute name="primaryIdentifier" type="java.lang.String"/>
    <attribute name="secondaryIdentifier" type="java.lang.String"/>
    <attribute name="name" type="java.lang.String"/>
    <reference name="organism" referenced-type="Organism"/>
    <collection name="children" referenced-type="BioEntity" />
    <collection name="parents" referenced-type="BioEntity" />
    <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/>
    <collection name="synonyms" referenced-type="Synonym" reverse-reference="subject"/>
    <collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/>
    <collection name="publications" referenced-type="Publication"/>
  </class>

  <class name="Comment" is-interface="true">
    <attribute name="text" type="java.lang.String"/>
    <attribute name="type" type="java.lang.String"/>
  </class> 

  <class name="DataSource" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <attribute name="url" type="java.lang.String"/>
    <attribute name="description" type="java.lang.String"/>
    <collection name="dataSets" referenced-type="DataSet" reverse-reference="dataSource"/>
  </class>

  <class name="DataSet" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <attribute name="url" type="java.lang.String"/>
    <attribute name="description" type="java.lang.String"/>
    <attribute name="version" type="java.lang.String"/>
    <reference name="dataSource" referenced-type="DataSource" reverse-reference="dataSets"/>
    <collection name="bioEntities" referenced-type="BioEntity" reverse-reference="dataSets"/>
  </class>

  <class name="Gene" is-interface="true">
    <attribute name="symbol" type="java.lang.String"/>
    <attribute name="ncbiGeneNumber" type="java.lang.String"/>
    <collection name="proteins" referenced-type="Protein" reverse-reference="genes"/>
  </class>

	<class name="Location" is-interface="true">
    <attribute name="end" type="java.lang.Integer"/>
    <attribute name="start" type="java.lang.Integer"/>
    <attribute name="strand" type="java.lang.String"/>
    <reference name="feature" referenced-type="BioEntity"/>
    <reference name="locatedOn" referenced-type="BioEntity"/>
  </class>

  <class name="Ontology" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <attribute name="url" type="java.lang.String"/>
  </class>
  
  <class name="OntologyTerm" is-interface="true">
    <attribute name="identifier" type="java.lang.String"/>
    <attribute name="name" type="java.lang.String"/>
    <attribute name="description" type="java.lang.String"/>
    <attribute name="namespace" type="java.lang.String"/>
    <attribute name="obsolete" type="java.lang.Boolean"/>
    <reference name="ontology" referenced-type="Ontology"/>
    <collection name="relations" referenced-type="OntologyRelation" />
    <collection name="synonyms" referenced-type="OntologyTermSynonym" />
    <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="ontologyTerm" /> 
    <collection name="parents" referenced-type="OntologyTerm" /> 
  </class>

  <class name="OntologyRelation" is-interface="true">
    <reference name="parentTerm" referenced-type="OntologyTerm" />
    <reference name="childTerm" referenced-type="OntologyTerm" />
    <attribute name="relationship" type="java.lang.String"/>
    <attribute name="direct" type="java.lang.Boolean"/>
    <attribute name="redundant" type="java.lang.Boolean"/>
  </class>

  <class name="OntologyAnnotation" is-interface="true">
    <attribute name="qualifier" type="java.lang.String"/>
    <reference name="subject" referenced-type="BioEntity" reverse-reference="ontologyAnnotations"/>
    <collection name="dataSets" referenced-type="DataSet" />
    <collection name="publications" referenced-type="Publication" />
    <reference name="ontologyTerm" referenced-type="OntologyTerm" reverse-reference="ontologyAnnotations"/>
  </class>

  <class name="OntologyTermSynonym" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <attribute name="type" type="java.lang.String"/>
  </class>
  
  <class name="Organism" is-interface="true">
    <attribute name="genus" type="java.lang.String"/>
    <attribute name="taxonId" type="java.lang.Integer"/>
    <attribute name="species" type="java.lang.String"/>
    <attribute name="commonName" type="java.lang.String"/>
    <attribute name="shortName" type="java.lang.String"/>
    <attribute name="name" type="java.lang.String"/>
  </class>

  <class name="Protein" extends="BioEntity" is-interface="true">
    <attribute name="md5checksum" type="java.lang.String"/>
    <attribute name="primaryAccession" type="java.lang.String"/>
    <attribute name="length" type="java.lang.Integer"/>
    <attribute name="molecularWeight" type="java.lang.Integer"/>
    <reference name="sequence" referenced-type="Sequence"/>
    <collection name="genes" referenced-type="Gene" reverse-reference="proteins"/>
  </class>

  <class name="Publication" is-interface="true">
    <attribute name="title" type="java.lang.String"/>
    <attribute name="issue" type="java.lang.String"/>
    <attribute name="pubMedId" type="java.lang.String"/>
    <attribute name="pages" type="java.lang.String"/>
    <attribute name="year" type="java.lang.Integer"/>
    <attribute name="volume" type="java.lang.String"/>
    <attribute name="journal" type="java.lang.String"/>
    <attribute name="firstAuthor" type="java.lang.String"/>
    <collection name="authors" referenced-type="Author" reverse-reference="publications" />
  </class>

  <class name="Sequence" is-interface="true">
    <attribute name="residues" type="java.lang.String"/>
    <attribute name="length" type="int"/>
    <attribute name="md5checksum" type="java.lang.String"/>
  </class>

  <class name="SequenceFeature" extends="BioEntity" is-interface="true">
    <attribute name="symbol" type="java.lang.String"/>
  </class>

  <class name="SequenceOntologyTerm" extends="OntologyTerm" is-interface="true"/>

  <class name="Synonym" is-interface="true">
    <attribute name="value" type="java.lang.String"/>
    <attribute name="type" type="java.lang.String"/>
    <attribute name="isPrimary" type="java.lang.Boolean"/>
    <reference name="subject" referenced-type="BioEntity" reverse-reference="synonyms"/>
    <collection name="dataSets" referenced-type="DataSet"/>
  </class>

</model><commit_msg>feature.length<commit_after><?xml version="1.0"?>
<model name="genomic" package="org.intermine.model.bio">

  <class name="Author" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <collection name="publications" referenced-type="Publication" reverse-reference="authors"/>
  </class>

  <class name="BioEntity" is-interface="true">
    <attribute name="primaryIdentifier" type="java.lang.String"/>
    <attribute name="secondaryIdentifier" type="java.lang.String"/>
    <attribute name="name" type="java.lang.String"/>
    <reference name="organism" referenced-type="Organism"/>
    <collection name="children" referenced-type="BioEntity" />
    <collection name="parents" referenced-type="BioEntity" />
    <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/>
    <collection name="synonyms" referenced-type="Synonym" reverse-reference="subject"/>
    <collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/>
    <collection name="publications" referenced-type="Publication"/>
  </class>

  <class name="Comment" is-interface="true">
    <attribute name="text" type="java.lang.String"/>
    <attribute name="type" type="java.lang.String"/>
  </class> 

  <class name="DataSource" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <attribute name="url" type="java.lang.String"/>
    <attribute name="description" type="java.lang.String"/>
    <collection name="dataSets" referenced-type="DataSet" reverse-reference="dataSource"/>
  </class>

  <class name="DataSet" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <attribute name="url" type="java.lang.String"/>
    <attribute name="description" type="java.lang.String"/>
    <attribute name="version" type="java.lang.String"/>
    <reference name="dataSource" referenced-type="DataSource" reverse-reference="dataSets"/>
    <collection name="bioEntities" referenced-type="BioEntity" reverse-reference="dataSets"/>
  </class>

  <class name="Gene" is-interface="true">
    <attribute name="symbol" type="java.lang.String"/>
    <attribute name="ncbiGeneNumber" type="java.lang.String"/>
    <collection name="proteins" referenced-type="Protein" reverse-reference="genes"/>
  </class>

	<class name="Location" is-interface="true">
    <attribute name="end" type="java.lang.Integer"/>
    <attribute name="start" type="java.lang.Integer"/>
    <attribute name="strand" type="java.lang.String"/>
    <reference name="feature" referenced-type="BioEntity"/>
    <reference name="locatedOn" referenced-type="BioEntity"/>
  </class>

  <class name="Ontology" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <attribute name="url" type="java.lang.String"/>
  </class>
  
  <class name="OntologyTerm" is-interface="true">
    <attribute name="identifier" type="java.lang.String"/>
    <attribute name="name" type="java.lang.String"/>
    <attribute name="description" type="java.lang.String"/>
    <attribute name="namespace" type="java.lang.String"/>
    <attribute name="obsolete" type="java.lang.Boolean"/>
    <reference name="ontology" referenced-type="Ontology"/>
    <collection name="relations" referenced-type="OntologyRelation" />
    <collection name="synonyms" referenced-type="OntologyTermSynonym" />
    <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="ontologyTerm" /> 
    <collection name="parents" referenced-type="OntologyTerm" /> 
  </class>

  <class name="OntologyRelation" is-interface="true">
    <reference name="parentTerm" referenced-type="OntologyTerm" />
    <reference name="childTerm" referenced-type="OntologyTerm" />
    <attribute name="relationship" type="java.lang.String"/>
    <attribute name="direct" type="java.lang.Boolean"/>
    <attribute name="redundant" type="java.lang.Boolean"/>
  </class>

  <class name="OntologyAnnotation" is-interface="true">
    <attribute name="qualifier" type="java.lang.String"/>
    <reference name="subject" referenced-type="BioEntity" reverse-reference="ontologyAnnotations"/>
    <collection name="dataSets" referenced-type="DataSet" />
    <collection name="publications" referenced-type="Publication" />
    <reference name="ontologyTerm" referenced-type="OntologyTerm" reverse-reference="ontologyAnnotations"/>
  </class>

  <class name="OntologyTermSynonym" is-interface="true">
    <attribute name="name" type="java.lang.String"/>
    <attribute name="type" type="java.lang.String"/>
  </class>
  
  <class name="Organism" is-interface="true">
    <attribute name="genus" type="java.lang.String"/>
    <attribute name="taxonId" type="java.lang.Integer"/>
    <attribute name="species" type="java.lang.String"/>
    <attribute name="commonName" type="java.lang.String"/>
    <attribute name="shortName" type="java.lang.String"/>
    <attribute name="name" type="java.lang.String"/>
  </class>

  <class name="Protein" extends="BioEntity" is-interface="true">
    <attribute name="md5checksum" type="java.lang.String"/>
    <attribute name="primaryAccession" type="java.lang.String"/>
    <attribute name="length" type="java.lang.Integer"/>
    <attribute name="molecularWeight" type="java.lang.Integer"/>
    <reference name="sequence" referenced-type="Sequence"/>
    <collection name="genes" referenced-type="Gene" reverse-reference="proteins"/>
  </class>

  <class name="Publication" is-interface="true">
    <attribute name="title" type="java.lang.String"/>
    <attribute name="issue" type="java.lang.String"/>
    <attribute name="pubMedId" type="java.lang.String"/>
    <attribute name="pages" type="java.lang.String"/>
    <attribute name="year" type="java.lang.Integer"/>
    <attribute name="volume" type="java.lang.String"/>
    <attribute name="journal" type="java.lang.String"/>
    <attribute name="firstAuthor" type="java.lang.String"/>
    <collection name="authors" referenced-type="Author" reverse-reference="publications" />
  </class>

  <class name="Sequence" is-interface="true">
    <attribute name="residues" type="java.lang.String"/>
    <attribute name="length" type="int"/>
    <attribute name="md5checksum" type="java.lang.String"/>
  </class>

  <class name="SequenceFeature" extends="BioEntity" is-interface="true">
    <attribute name="symbol" type="java.lang.String"/>
    <attribute name="length" type="int"/>
  </class>

  <class name="SequenceOntologyTerm" extends="OntologyTerm" is-interface="true"/>

  <class name="Synonym" is-interface="true">
    <attribute name="value" type="java.lang.String"/>
    <attribute name="type" type="java.lang.String"/>
    <attribute name="isPrimary" type="java.lang.Boolean"/>
    <reference name="subject" referenced-type="BioEntity" reverse-reference="synonyms"/>
    <collection name="dataSets" referenced-type="DataSet"/>
  </class>

</model>
{'fraction_non_alphanumeric': 0.1799373497486705, 'fraction_numerical': 0.0005827930356232243, 'mean_word_length': 5.251366120218579, 'pattern_counts': {'":': 0, '<': 256, '<?xml version=': 2, '>': 256, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '718405', 'n_tokens_mistral': 4102, 'n_tokens_neox': 3949, 'n_words': 714}