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[bioontology-support] [BioPortal] Feedback from Thomas Lemberger

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Apr 27 15:59:21 PDT 2020


Hi Thomas,

Thank you for providing additional detail. Please see my answers inline below.


On Apr 27, 2020, at 1:18 PM, Thomas Lemberger <thomas.lemberger at embo.org<mailto:thomas.lemberger at embo.org>> wrote:

Dear Jennifer,

Many thanks for getting back to me and apologies if my description was confusing. Maybe it is just my misunderstanding.

Let’s take the example of the term bao:BAO_0002424 for the assay ‘western blot’.

In the CSV file (http://data.bioontology.org/ontologies/BAO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=csv), ‘western blot’ is described in row 172

Class ID        Preferred Label Synonyms        Definitions     Obsolete        CUI     Semantic Types  Parents alternative term        alternative_term        axiom_lost_from_external_ontology       based on normalization  bearer of       catalyzed by    connected to    contains process        contributor     curator notes   database_cross_reference        definition      definition      definition source       derives from    derives into    detects detects phenotype       development_notes       editor note     editor preferred term~editor preferred label    encodes example of usage        external_definition     external_ontology_notes fma_set_term    function_notes  has absorbance wavelength value has activity threshold value    has alternate assay conditions  has alternate assay format      has alternate assay type        has alternate cell line assay   has alternate confirmatory assay        has alternate organism assay    has alternate target assay      has anti-sense strand sequence  has antibody source     has artificial regulatory region copy number    has assay control       has assay deposition date       has assay design method has assay footprint     has assay format        has assay kit   has assay kit component has assay medium        has assay method        has assay phase characteristic  has assay pressure value        has assay protocol      has assay readout content       has assay readout content parametricity has assay readout type  has assay serum has assay source        has assay stage has assay supporting method     has assay temperature value     has assay title has associated disease  has binding site        has bioassay type       has biosafety level     has cDNA copy number    has cell count  has cell line   has cell modification temperature value has cell modification time value        has compound aggregation assay  has compound fluorescence assay has compound redox-activity assay       has compound toxicity assay     has concentration       has concentration throughput    has concentration unit  has confirmatory assay  has copy number has counter assay       has coupled substrate incubation temperature value      has coupled substrate incubation time value     has curation status     has curve fit specification     has detected entity     has detection method    has DNA sequence        has emission wavelength value   has endpoint    has endpoint modifier   has enzyme reaction temperature value   has enzyme reaction time value  has excitation wavelength value has form        has function    has function in has gene symbol has id value    has identical assay     has incubation time value       has indicator   has inducer     has lead optimization assay     has ligand incubation time value        has manufacturer        has marker      has measure group       has measured entity     has mode of action      has molecular phenotype has morphological phenotype     has negative control    has nucleic acid sequence       has organism    has orthogonal assay design     has orthogonal assay technology has parental cell line assay    has part        has participant has passage number      has percent response    has percent response value      has perturbagen has perturbagen incubation temperature value    has perturbagen incubation time value   has phenotype   has physicochemical profiling assay     has positive control    has preparation method  has primary assay       has protein sequence    has purity unit has quality     has recommended name    has repetition point-number     has repetition throughput       has response unit       has response value      has RNA sequence        has role        has selectivity assay   has sense strand sequence       has sequence    has sequence position   has shRNA probe sense sequence position has shRNA sense sequence        has signal direction    has siRNA probe sense sequence position has specification       has substrate   has substrate incubation temperature value      has substrate incubation time value     has summary assay       has target      has temperature unit    has temperature value   has time unit   has transcription factor        has unit        has value       has variant construct assay     has wavelength value    has_alternative_id      has_broad_synonym       has_exact_synonym       has_narrow_synonym      has_obo_namespace       has_related_synonym     has_relational_adjective        homology_notes  http://data.bioontology.org/metadata/prefixIRI  http://purl.obolibrary.org/obo/hasDbXref        http://purl.obolibrary.org/obo/hasOBONamespace  http://purl.obolibrary.org/obo/IAO_0000231      http://purl.obolibrary.org/obo/id       http://purl.obolibrary.org/obo/is_metadata_tag  http://purl.obolibrary.org/obo/RO_0002161       http://purl.obolibrary.org/obo/RO_0002174       http://purl.obolibrary.org/obo/shorthand        http://purl.obolibrary.org/obo/uberon/core#dubious_for_taxon    http://purl.obolibrary.org/obo/uberon/core#fma_set_term http://purl.obolibrary.org/obo/uberon/core#homologous_in        http://purl.obolibrary.org/obo/uberon/core#spatially_disjoint_from      http://purl.org/dc/elements/1.1/date    http://purl.org/dc/elements/1.1/license http://purl.org/dc/elements/1.1/relation        http://purl.org/dc/elements/1.1/source  http://www.ebi.ac.uk/cellline/definition        http://www.ebi.ac.uk/cellline/definition_editor http://www.ebi.ac.uk/efo/bioportal_provenance   http://www.ebi.ac.uk/efo/definition_citation    http://www.ebi.ac.uk/efo/EV_definition_citation http://www.ebi.ac.uk/efo/EVM_definition_citation        http://www.ebi.ac.uk/efo/FBdv_definition_citation       http://www.ebi.ac.uk/efo/MAT_definition_citation        http://www.ebi.ac.uk/efo/MSH_definition_citation        http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation      http://www.ebi.ac.uk/efo/NIFSTD_definition_citation     http://www.ebi.ac.uk/efo/obsoleted_in_version   http://www.ebi.ac.uk/efo/organizational_class   http://www.ebi.ac.uk/efo/reason_for_obsolescence        http://www.ebi.ac.uk/efo/SNOMEDCT_definition_citation   http://www.ebi.ac.uk/efo/WBls_definition_citation       http://www.ebi.ac.uk/efo/XAO_definition_citation        http://www.ebi.ac.uk/efo/ZFS_definition_citation        http://www.geneontology.org/formats/oboInOwl#created_by http://www.geneontology.org/formats/oboInOwl#creation_date      http://www.geneontology.org/formats/oboInOwl#hasDefinition      http://www.geneontology.org/formats/oboInOwl#id http://www.geneontology.org/formats/oboInOwl#is_class_level     http://www.geneontology.org/formats/oboInOwl#is_metadata_tag    http://www.w3.org/2000/01/rdf-schema#comment    http://www.w3.org/2000/01/rdf-schema#isDefinedBy        http://www.w3.org/2000/01/rdf-schema#seeAlso    http://www.w3.org/2002/07/owl#deprecated        http://www.w3.org/2002/07/owl#topDataProperty   http://www.w3.org/2002/07/owl#topObjectProperty http://www.w3.org/2004/02/skos/core#notation    http://xmlns.com/foaf/0.1/depicted_by   imported from   in_subset       inheres in      involves biological process     involves molecular function     is alternate assay conditions of        is alternate assay format of    is alternate assay type of      is alternate cell line assay of is alternate confirmatory assay of      is alternate organism assay of  is alternate target assay of    is assay format of      is assay method of      is assay protocol of    is associated disease of        is binding site of      is bioassay type of     is cell line of is compound aggregation assay of        is compound fluorescence assay of       is compound redox-activity assay of     is compound toxicity assay of   is confirmatory assay of        is counter assay of     is derived from is described by is detected by  is detection method of  is endpoint of  is grown in     is identical assay of   is indicator of is input data value of  is lead optimization assay of   is localized in is marker of    is measure group of     is measured entity of   is opposite_of  is orthogonal assay design of   is orthogonal assay technology of       is parental cell line assay of  is perturbagen of       is phenotype of is physicochemical profiling assay of   is primary assay of     is regulated by is regulator of is related assay to     is role of      is selectivity assay of is specification of     is substrate of is summary assay of     is target of    is transfected into     is unit of      is variant construct assay of   label   LINCS ID        occurs in       part of participates in phenotype of    PubChem AID     quantifies      recombinantly expressed in      reports reports assay measurment value  shorthand       silences        stains  structure_notes taxon_notes     term editor     term replaced by        uses as substrate       uses assay kit  uses detection instrument
http://www.bioassayontology.org/bao#BAO_0002424 western blot            The western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.     FALSE                   http://www.bioassayontology.org/bao#BAO_0002422                                                         The western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     bao:BAO_0002424                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 western blot



I think this term is absent from the owl file (http://data.bioontology.org/ontologies/BAO/submissions/36/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb).


The ontology source file for BAO (bao_complete.owl) has two import statements near the top of the file:

<owl:imports rdf:resource="http://www.bioassayontology.org/bao/bao_core.owl"/>
<owl:imports rdf:resource="http://www.bioassayontology.org/bao/bao_external.owl"/>

At processing time, BioPortal reads those import statements and dynamically pulls in the content from the imported ontologies. So, yes - you are correct that the “western blot” term doesn’t appear in the root ontology (bao_complete.owl). However, it does appear in one of the ontologies that BAO imports, which is why you see that data in BioPortal. The BAO ontology has a fairy complicated import structure. I opened it in the Protege ontology editor (https://protege.stanford.edu/) where you can see a graphical representations of the imports:


[cid:F2D14877-A216-4A61-901D-300DB8CACA4E at stanford.edu]


Furthermore, other terms that are in the owl file, for example bao:BAO_0000978 “NP-40” seem to include only the class/sub class hierarchy but no other information (no definition, no label etc…)

<!-- http://www.bioassayontology.org/bao#BAO_0000978 -->
<owl:Class rdf:about="http://www.bioassayontology.org/bao#BAO_0000978">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0003102"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_27780"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>

The equivalent term in the CSV (row 1640) is:

Class ID        Preferred Label Synonyms        Definitions     Obsolete        CUI     Semantic Types  Parents alternative term        alternative_term        axiom_lost_from_external_ontology       based on normalization  bearer of       catalyzed by    connected to    contains process        contributor     curator notes   database_cross_reference        definition      definition      definition source       derives from    derives into    detects detects phenotype       development_notes       editor note     editor preferred term~editor preferred label    encodes example of usage        external_definition     external_ontology_notes fma_set_term    function_notes  has absorbance wavelength value has activity threshold value    has alternate assay conditions  has alternate assay format      has alternate assay type        has alternate cell line assay   has alternate confirmatory assay        has alternate organism assay    has alternate target assay      has anti-sense strand sequence  has antibody source     has artificial regulatory region copy number    has assay control       has assay deposition date       has assay design method has assay footprint     has assay format        has assay kit   has assay kit component has assay medium        has assay method        has assay phase characteristic  has assay pressure value        has assay protocol      has assay readout content       has assay readout content parametricity has assay readout type  has assay serum has assay source        has assay stage has assay supporting method     has assay temperature value     has assay title has associated disease  has binding site        has bioassay type       has biosafety level     has cDNA copy number    has cell count  has cell line   has cell modification temperature value has cell modification time value        has compound aggregation assay  has compound fluorescence assay has compound redox-activity assay       has compound toxicity assay     has concentration       has concentration throughput    has concentration unit  has confirmatory assay  has copy number has counter assay       has coupled substrate incubation temperature value      has coupled substrate incubation time value     has curation status     has curve fit specification     has detected entity     has detection method    has DNA sequence        has emission wavelength value   has endpoint    has endpoint modifier   has enzyme reaction temperature value   has enzyme reaction time value  has excitation wavelength value has form        has function    has function in has gene symbol has id value    has identical assay     has incubation time value       has indicator   has inducer     has lead optimization assay     has ligand incubation time value        has manufacturer        has marker      has measure group       has measured entity     has mode of action      has molecular phenotype has morphological phenotype     has negative control    has nucleic acid sequence       has organism    has orthogonal assay design     has orthogonal assay technology has parental cell line assay    has part        has participant has passage number      has percent response    has percent response value      has perturbagen has perturbagen incubation temperature value    has perturbagen incubation time value   has phenotype   has physicochemical profiling assay     has positive control    has preparation method  has primary assay       has protein sequence    has purity unit has quality     has recommended name    has repetition point-number     has repetition throughput       has response unit       has response value      has RNA sequence        has role        has selectivity assay   has sense strand sequence       has sequence    has sequence position   has shRNA probe sense sequence position has shRNA sense sequence        has signal direction    has siRNA probe sense sequence position has specification       has substrate   has substrate incubation temperature value      has substrate incubation time value     has summary assay       has target      has temperature unit    has temperature value   has time unit   has transcription factor        has unit        has value       has variant construct assay     has wavelength value    has_alternative_id      has_broad_synonym       has_exact_synonym       has_narrow_synonym      has_obo_namespace       has_related_synonym     has_relational_adjective        homology_notes  http://data.bioontology.org/metadata/prefixIRI  http://purl.obolibrary.org/obo/hasDbXref        http://purl.obolibrary.org/obo/hasOBONamespace  http://purl.obolibrary.org/obo/IAO_0000231      http://purl.obolibrary.org/obo/id       http://purl.obolibrary.org/obo/is_metadata_tag  http://purl.obolibrary.org/obo/RO_0002161       http://purl.obolibrary.org/obo/RO_0002174       http://purl.obolibrary.org/obo/shorthand        http://purl.obolibrary.org/obo/uberon/core#dubious_for_taxon    http://purl.obolibrary.org/obo/uberon/core#fma_set_term http://purl.obolibrary.org/obo/uberon/core#homologous_in        http://purl.obolibrary.org/obo/uberon/core#spatially_disjoint_from      http://purl.org/dc/elements/1.1/date    http://purl.org/dc/elements/1.1/license http://purl.org/dc/elements/1.1/relation        http://purl.org/dc/elements/1.1/source  http://www.ebi.ac.uk/cellline/definition        http://www.ebi.ac.uk/cellline/definition_editor http://www.ebi.ac.uk/efo/bioportal_provenance   http://www.ebi.ac.uk/efo/definition_citation    http://www.ebi.ac.uk/efo/EV_definition_citation http://www.ebi.ac.uk/efo/EVM_definition_citation        http://www.ebi.ac.uk/efo/FBdv_definition_citation       http://www.ebi.ac.uk/efo/MAT_definition_citation        http://www.ebi.ac.uk/efo/MSH_definition_citation        http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation      http://www.ebi.ac.uk/efo/NIFSTD_definition_citation     http://www.ebi.ac.uk/efo/obsoleted_in_version   http://www.ebi.ac.uk/efo/organizational_class   http://www.ebi.ac.uk/efo/reason_for_obsolescence        http://www.ebi.ac.uk/efo/SNOMEDCT_definition_citation   http://www.ebi.ac.uk/efo/WBls_definition_citation       http://www.ebi.ac.uk/efo/XAO_definition_citation        http://www.ebi.ac.uk/efo/ZFS_definition_citation        http://www.geneontology.org/formats/oboInOwl#created_by http://www.geneontology.org/formats/oboInOwl#creation_date      http://www.geneontology.org/formats/oboInOwl#hasDefinition      http://www.geneontology.org/formats/oboInOwl#id http://www.geneontology.org/formats/oboInOwl#is_class_level     http://www.geneontology.org/formats/oboInOwl#is_metadata_tag    http://www.w3.org/2000/01/rdf-schema#comment    http://www.w3.org/2000/01/rdf-schema#isDefinedBy        http://www.w3.org/2000/01/rdf-schema#seeAlso    http://www.w3.org/2002/07/owl#deprecated        http://www.w3.org/2002/07/owl#topDataProperty   http://www.w3.org/2002/07/owl#topObjectProperty http://www.w3.org/2004/02/skos/core#notation    http://xmlns.com/foaf/0.1/depicted_by   imported from   in_subset       inheres in      involves biological process     involves molecular function     is alternate assay conditions of        is alternate assay format of    is alternate assay type of      is alternate cell line assay of is alternate confirmatory assay of      is alternate organism assay of  is alternate target assay of    is assay format of      is assay method of      is assay protocol of    is associated disease of        is binding site of      is bioassay type of     is cell line of is compound aggregation assay of        is compound fluorescence assay of       is compound redox-activity assay of     is compound toxicity assay of   is confirmatory assay of        is counter assay of     is derived from is described by is detected by  is detection method of  is endpoint of  is grown in     is identical assay of   is indicator of is input data value of  is lead optimization assay of   is localized in is marker of    is measure group of     is measured entity of   is opposite_of  is orthogonal assay design of   is orthogonal assay technology of       is parental cell line assay of  is perturbagen of       is phenotype of is physicochemical profiling assay of   is primary assay of     is regulated by is regulator of is related assay to     is role of      is selectivity assay of is specification of     is substrate of is summary assay of     is target of    is transfected into     is unit of      is variant construct assay of   label   LINCS ID        occurs in       part of participates in phenotype of    PubChem AID     quantifies      recombinantly expressed in      reports reports assay measurment value  shorthand       silences        stains  structure_notes taxon_notes     term editor     term replaced by        uses as substrate       uses assay kit  uses detection instrument
http://www.bioassayontology.org/bao#BAO_0000978 NP-40           NP-40 is a commercially available detergent. The full name of NP-40 is Tergitol-type NP-40, which is nonyl phenoxypolyethoxylethanol.   FALSE                   http://www.bioassayontology.org/bao#BAO_0003043                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         bao:BAO_0000978                                                                                                                                                                                                                                                                                                                         NP-40 is a commercially available detergent. The full name of NP-40 is Tergitol-type NP-40, which is nonyl phenoxypolyethoxylethanol.                                                                                                                                                                                                                                                                                                                                                                                                                                                                           NP-40



This is the same situation where the definition is formally declared not in the root ontology, but in one of the ontologies that BAO imports. The BioPortal user interface doesn’t present any information that would help you track down which import the declaration lives in - for that, you would need to use a different tool. If you’re familiar with the Protege application that I mentioned above, you could use the following steps:

1). Open bao_complete.owl
2). Click the Search… button in the top right corner and enter NP-40 in the resulting Search dialog
3). Double click the first match in the result list:

[cid:EC6287D3-3CBC-4901-9D73-784E9E973719 at stanford.edu]

This will navigate to NP-40 in the classes tree where you can view all of the properties attached to the class. If you hover your mouse over the rdfs:comment on the right-hand side in the Class Annotations pane, you’ll see a tooltip pop up that will tell you where the comment was declared. In this case, I see tooltip content of “Asserted in: http://www.bioassayontology.org/bao/bao_vocabulary_materialentity.owl”.


In the meantime, I found that the RDF/XML file http://data.bioontology.org/ontologies/BAO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=rdf includes the entire ontology, so I am not sure what is the role of the .owl file in the case of BAO. This seems to be different with other ontologies I downloaded.

Maybe I am just misunderstanding something.


The OWL file is the canonical source file that was submitted to BioPortal by the ontology maintainer. The RDF/XML file is generated by BioPortal at processing time and includes everything from the original ontology source file, as well as data from imported ontologies. BioPortal is backed by an RDF store, so we need to have this intermediate step of generating an RDF/XML representation from the various ontology formats that end users are allowed to submit (OWL, OBO, and SKOS).


In the case of other ontologies, for example OBI https://bioportal.bioontology.org/ontologies/OBI, the .owl file (http://data.bioontology.org/ontologies/OBI/submissions/42/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb) does include the whole ontology and not only the class/subclass hierarchy.


I checked OBI and it doesn’t have any imports, which is why the entirety of the ontology content is visible in the original source OWL file.

Hope this information is helpful.

Kind regards,
Jennifer



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