Skip to content

Commit

Permalink
Added two new sequencing technologies required for HCA
Browse files Browse the repository at this point in the history
  • Loading branch information
@daniwelter
daniwelter committed Aug 13, 2018
1 parent 7bcd46a commit 7bbf453
Showing 1 changed file with 44 additions and 4 deletions.
48 changes: 44 additions & 4 deletions src/ontology/efo-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -487195,7 +487195,7 @@ label: granulocyte colony-stimulating factor measurement</reason_for_obsolescenc
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Single G2/M nucleus sequencing of cells in S phase (Nuc-seq)</obo:IAO_0000115>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Single G2/M nucleus sequencing of cells in S phase (nuc-seq)</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dani Welter</obo:IAO_0000117>
<PMID_definition_citation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:25079324</PMID_definition_citation>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nuc-seq</rdfs:label>
Expand Down Expand Up @@ -491674,7 +491674,6 @@ label: granulocyte colony-stimulating factor measurement</reason_for_obsolescenc
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dani Welter</obo:IAO_0000117>
<alternative_term>10X</alternative_term>
<alternative_term>10x</alternative_term>
<alternative_term>10x_v2</alternative_term>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10X sequencing</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -503974,6 +503973,47 @@ It allows sampling of specific cells under direct microscopic visualization by a



<!-- http://www.ebi.ac.uk/efo/EFO_0009309 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009309">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000308"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000275"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/obo/owl/OBO_REL#role_of"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33697"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Div-Seq is a single-nucleus RNA sequencing technique that improves upon sNuc-Seq by incorporating 5-ethynyl-2’-deoxyuridine (EdU) labeling to identify dividing cells during their different cell stages. EdU labeling also enables identification of different cell types in complex tissue samples and rare cell populationsduring FACS. Briefly, samples are labeled in vivo with EdU, dissected, and fixed before isolation into single nuclei. Individual nuclei are tagged fluorescently and sorted by FACS. From this step, the procedure follows the Nuc-Seq method: cDNA synthesis is performed using the Smart-seq2 protocol, while the cDNA library is prepared with Tn5 transposase–mediated tagmentation.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dani Welter</obo:IAO_0000117>
<PMID_definition_citation>PMID:27471252</PMID_definition_citation>
<rdfs:label>Div-Seq</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_0009310 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009310">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0008995"/>
<obo:IAO_0000115>10x v2 is the second version of the 10x sequencing technology.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dani Welter</obo:IAO_0000117>
<alternative_term>10x v2</alternative_term>
<alternative_term>10x_v2</alternative_term>
<rdfs:label>10X v2 sequencing</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_1000003 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_1000003">
Expand Down Expand Up @@ -720186,8 +720226,8 @@ In EFO&apos;s scope, an obsolete class that holds an external-ontology namespace
<oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_proximal_side_of</oboInOwl:shorthand>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X proximal_side_of Y &lt;=&gt; if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.</obo:IAO_0000115>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_proximal_side_of</rdfs:label>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_proximal_side_of</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_proximal_side_of</rdfs:label>
</rdf:Description>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BSPO_0000124"/>
Expand All @@ -720197,9 +720237,9 @@ In EFO&apos;s scope, an obsolete class that holds an external-ontology namespace
</owl:Axiom>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BSPO_0000125">
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BSPO:0000125</oboInOwl:hasDbXref>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_distal_side_of</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_distal_side_of</rdfs:label>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X distal_side_of Y &lt;=&gt; if Y is subdivided into distal and proximal portions, X is part_of the distal portion.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_distal_side_of</oboInOwl:id>
<oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_distal_side_of</oboInOwl:shorthand>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
</rdf:Description>
Expand Down

0 comments on commit 7bbf453

Please sign in to comment.