Adding nanomaterial data

Adding nanomaterial data to an eNanoMapper instance can be done in many different ways, as one would expect in a open platform. Data can be entered using the JRC spreadsheet formats, using R code and the eNanoMapper application programming interface (API), and, as done in this tutorial in the Resource Description Framework (RDF) format, using a schema based on various ontologies.

This tutorial expects some basic knowledge about RDF, particularly, the concept of IRIs and triples. The examples used will illustrate a lot, but does not replace reading up on RDF literature. If new to this, and if something in not clear when you go through the tutorial below, you consider reading RDF 1.1 Turtle - Terse RDF Triple Language.

Furthermore, because RDF is a semantic format, it will rely on the eNanoMapper ontology. At various places it will link to the EMBL-EBI Ontology Lookup Service (OLS) to show a term. Besides the OLS BioPortal can be used to browse the ontology too. The reader may be interested in the Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé tutorial.

Turtle and namespaces

To shorten the RDF statements in this tutorial, it will depend on the use of namespace. The following two documents are identical, using the @prefix command to define the namespaces:

<https://nanocommons.github.io/tutorials/demo/owner/NT18-DS> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>  <http://rdfs.org/ns/void#Dataset> .

and

@prefix owner: <https://nanocommons.github.io/tutorials/demo/owner/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix void:  <http://rdfs.org/ns/void#> .
@prefix dcterms: <http://purl.org/dc/terms/> .

owner:NT18-DS rdf:type void:Dataset .

Because rdf:type is frequently used, the Turtle standard allows it to be shortened to a mere a, so that the triple can be further shortened to (just the triple, so ommiting the namespace declarations):

owner:NT18-DS a void:Dataset .

Namespaces used in this tutorial

Because using namespaces makes the RDF more readable, this tutorial uses the following namespaces:

@prefix bao:   <http://www.bioassayontology.org/bao#> .
@prefix cito:  <http://purl.org/net/cito/> .
@prefix dc:    <http://purl.org/dc/elements/1.1/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix foaf:  <http://xmlns.com/foaf/0.1/> .
@prefix npo:   <http://purl.bioontology.org/ontology/npo#> .
@prefix obo:   <http://purl.obolibrary.org/obo/> .
@prefix owner: <https://nanocommons.github.io/tutorials/demo/owner/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sio:   <http://semanticscience.org/resource/> .
@prefix void:  <http://rdfs.org/ns/void#> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .

Adding a dataset

The first thing to do is define a dataset. The eNanoMapper software will read this as a bundle. Each dataset has license statement, the name of the distributor (which is often different from the copyright owner), a description (the @en annotation indicated the language), and a title. For example:

owner:NT18-DS
        a                   void:Dataset ;
        dcterms:license     <https://creativecommons.org/publicdomain/zero/1.0/> ;
        dcterms:publisher   "Egon Willighagen"@en ;
        dcterms:description "Nanomaterials I am excited about."@en ;
        dcterms:title       "Exciting nanomaterials"@en .

Possible license IRIs include:

Adding a nanomaterial

But at this moment, the dataset is still empty. We did not add nanomaterials to it. The very minimal amount of information is that the nanomaterial is a chemical substance, and for that we will use the chemical substance term from the eNanoMapper ontology (CHEBI_59999). Furthermore, we will give the material a name and a ontology annotation, for which we also use the eNanoMapper ontology (here, a NPO_1542):

owner:NT18-S1
        a                obo:CHEBI_59999 ;
        rdfs:label       "zinc oxide" ;
        dcterms:source   owner:NT18-DS ;
        dcterms:type     npo:NPO_1542 .

This example is taken from a recent paper by the HINAMOX project (doi:10.3390/ijms19010246).

To figure out what type of nanomaterial you have, you can browse the eNanoMapper ontology (see the aforementioned tutorial). If you are using any of the OECD or JRC nanomaterials, you are lucky and can also use one of these two guidance documents:

Use Case: linking to third party databases

The above information does not sounds like a lot yet, but can still be useful. Say you have some data collection online, with one web page for each material, and you want the eNanoMapper database to link to that. The above would be enough, except that we would need to add the link to that web page. That can be done with the FOAF ontology:

owner:NT18-S1 foaf:page <http://www.mdpi.com/1422-0067/19/1/246/htm>

For the running example, the page linked to is not specifically about that nanomaterial, but the page of the full article.

Adding some chemistry

There is plenty of room at the bottom, and that applies to this story too. The above basically only covers the name of the compound, along with some metadata. Let’s describe next what we know about the chemical content of the material.

First, the full composition is modelled after the NPO ontology and each nanoparticle has parts, so if we want to define a core part, we create a new resource for that, with out unique IRI, and link that to the nanoparticle with npo:has_part.

The core

Let’s first define the core of that nanomaterial. For this we define a new resource, for the core, and type it as a core using a term from the NPO ontology NPO

owner:NT18-S1_core  a           npo:NPO_1597 ;
        sio:CHEMINF_000200  owner:NT18-S1_core_smiles .

owner:NT18-S1_core_smiles
        a               sio:CHEMINF_000018 ;
        rdfs:label      "zinc oxide" ;
        sio:SIO_000300  "ZnO" .

In the above example, we used the NPO_1597 term for fiat material part.

We can further annotate the material part, by adding a triple to indicate the part is actually a core with NPO_1617:

owner:NT18-S1_core a    npo:NPO_1617 .

Alternative ontology annotations for cores from the eNanoMapper ontology (inherited from the NanoPartical Ontology) include:

See the full hierarchy for more possible annotation.

The coating

A coating is added as fiat material part too, and follows the same approach as the core.

Impurities

Adding physical-chemical properties

We can also add physical-chemical properties to the data, further characterizing the nanomaterial. For both physical-chemical and biological properties, the data model is reused introduced in the PubChem RDF (see also doi:10.1186/s13321-015-0084-4) and using various ontologies:

Two examples

Here are two examples of physical chemical endpoints. In fact, we can use physical property endpoint (BAO_0002128) instead of endpoint of which it is a subclass.

Primary particle size

For example, for a particle size (NPO_1694), we get the following set up:

owner:NFYS16-M12
        obo:BFO_0000056  owner:NFYS16-M12_sizemg .

owner:NFYS16-sizeAssay1
        a                npo:NPO_1694 , bao:BAO_0000015 ;
        dc:title         "Particle Size" ;
        bao:BAO_0000209  owner:NFYS16-M12_sizemg .

owner:NFYS16-M12_sizemg  a  obo:BAO_0000040 ;
        obo:OBI_0000299  owner:NFYS16-M12_size .

owner:NFYS16-M12_size  a    bao:BAO_0002128 ;
        rdfs:label       "primary particle size" ;
        sio:has-unit     "nm" ;
        sio:has-value    "13.6" .

Note: the above is ontologically not entirely correct, as NPO_1694 is not actually an assay type, but a quality.

A citation to the article which describes the physicochemical properties can be added to the endpoint, which would make the last block look like:

owner:NFYS16-M12_size  a  bao:BAO_0002128 ;
        rdfs:label        "primary particle size" ;
        sio:has-unit      "nm" ;
        sio:has-value     "13.6" ;
        cito:usesDataFrom <https://doi.org/10.1021/es900754q> .

Zeta potential

Similarly, for a zeta potential

owner:NFYS16-M12
        obo:BFO_0000056  owner:NFYS16-M12_zpmg .

owner:NFYS16-sizeAssay2
        a                npo:NPO_1302 , bao:BAO_0000015 ;
        dc:title         "Zeta Potential" ;
        bao:BAO_0000209  ex:NFYS16-M12_zpmg .

owner:NFYS16-M12_zpmg  a  obo:BAO_0000040 ;
        obo:OBI_0000299  owner:NFYS16-M12_zp .

owner:NFYS16-M12_zp  a        bao:BAO_0002128 ;
        rdfs:label         "ZETA POTENTIAL" ;
        obo:STATO_0000035  "-53.5 ± 10.6"^^xsd:string ;
        sio:has-unit       "mV" .

Alternatives for adding measurement values

The above two examples indicated two different ways to provide the measured value of the end point. In both cases there was a single value, but one had an indication of the measurement error. The system supports currently the following patterns.

First, a single value:

owner:NFYS16-M12_zp  a        bao:BAO_0000179 ;
        sio:has-value    "13.6"^^xsd:double .

Secondly, a single value with error indication, using a predicate from the STATO:

owner:NFYS16-M12_zp  a        bao:BAO_0000179 ;
        obo:STATO_0000035  "-53.5 ± 10.6"^^xsd:string .

The third option is to define a minimum and maximum:

owner:NFYS16-M12_zp  a        bao:BAO_0000179 ;
        obo:STATO_0000035  "1-10"^^xsd:string ; .

Adding biological endpoints

A biological endpoints is modelled similarly to a physical-chemical endpoint. But currently, the ontological type of quality measured is given on the endpoint, not on the assay. For example,

owner:m134_noecMeasurementGroup533
        a                bao:BAO_0000040 ;
        obo:OBI_0000299  owner:m134_noecMeasurementGroup533_noecEndpoint .

owner:m134_noecMeasurementGroup533_noecEndpoint
        a                enm:ENM_0000060 ;
        rdfs:label       "NOEC" ;
        obo:IAO_0000136  etox:m134 ;
        sio:has-unit     "µg/L" ;
        sio:has-value    "15"^^xsd:double .

Uploading to eNanoMapper

The upload page

In this tutorial we will use a test server with the eNanoMapper server provided by IDEAConsult Ltd., where we can upload any test data: https://apps.ideaconsult.net/enmtest/.

The September 2018 version of the eNanoMapper database software contains a dedicated upload page for the here introduced Turtle:

Screenshot of Turtle upload page

With the “Choose File” button, you can select your newly created Turtle file, followed by clicking the Submit button.

The next page will show information of the running task, reflecting the reading of the data. If your Turtle validated (see the previous step), you should not get an error message. If all indeed loaded well, you will get a link to one of the materials loaded.

Inspecting the results

However, to see the full collection, we can better go to the Bundles page, which should list your new bundle too. If there are many bundles listed, you can search your bundle using the title you provided:

Using the Search functionality to restrict the number of bundles shown.

If you click the folder icon in the first column, in the row for your bundle, you will get a link to a list with all Substances. That way you can verify that all your materials were read in properly.

Acknowledgments

This tutorial was written as part of the NanoCommons project. NanoCommons (Grant Agreement 731032) is a project funded by the European Commission within Horizon2020 Programme