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"http://emmo.info/electrochemistry#electrochemistry_d0a26dc2_fde9_4a11_ac26_7c18499d28a5", + "ZincFlowBattery": "http://emmo.info/battery#battery_5afce525_90b7_4807_87f0_ab23a52a0320", + "ZincFluoride": "https://w3id.org/emmo/domain/chemicalsubstance#substance_be030e60_3df6_4147_ba07_c99618bed3fb", + "ZincHexafluorophosphate": "https://w3id.org/emmo/domain/chemicalsubstance#substance_a4e68f0a_07b5_4899_b570_f3a70a07b5b3", + "ZincHydroxide": "https://w3id.org/emmo/domain/chemicalsubstance#substance_177b95f8_2816_43de_94bb_1a1054c45e32", + "ZincInsertionElectrode": "http://emmo.info/electrochemistry#electrochemistry_245c9442_ca1d_4070_a624_182b92d30b10", + "ZincIodide": "https://w3id.org/emmo/domain/chemicalsubstance#substance_761c90b7_61f7_495a_a5e7_a00afb14e41f", + "ZincNitrate": "https://w3id.org/emmo/domain/chemicalsubstance#substance_e1bfc0f5_7192_49f2_9ce1_1be2467e0b7a", + "ZincNitrite": "https://w3id.org/emmo/domain/chemicalsubstance#substance_db926a48_0b3c_4f6d_89f5_a333af85ecbd", + "ZincOxide": "https://w3id.org/emmo/domain/chemicalsubstance#substance_848003a2_71ee_4967_8039_354c907ec7f4", + "ZincOxideCompound": "https://w3id.org/emmo/domain/chemicalsubstance#substance_28754642_a1ed_4f39_8b00_2c7857336bab", + "ZincOxideElectrode": "http://emmo.info/electrochemistry#electrochemistry_82c70935_0aea_454b_92bf_17fb0b488012", + "ZincPerchlorate": "https://w3id.org/emmo/domain/chemicalsubstance#substance_413d32e9_2ec2_474a_9ddb_48277920ba21", + "ZincPhosphate": "https://w3id.org/emmo/domain/chemicalsubstance#substance_51e414c6_e619_446c_898a_dac0f4855584", + "ZincSaltCompound": "https://w3id.org/emmo/domain/chemicalsubstance#substance_b07a5287_67d1_4f4f_9640_e0146f713a6c", + "ZincShuttleBattery": "http://emmo.info/battery#battery_b023508b_62eb_4b7d_9b4d_0715be990dd8", + "ZincSilverOxideBattery": "http://emmo.info/battery#battery_b81610fd_0bce_411b_986e_f3b4f3f562ab", + "ZincSulfate": "https://w3id.org/emmo/domain/chemicalsubstance#substance_91890364_2be0_4333_ae45_f619cbf2d078", + "ZincSulfide": "https://w3id.org/emmo/domain/chemicalsubstance#substance_59db0926_27f3_444d_b3b7_126e9ea0b8e3", + "ZincSulfite": "https://w3id.org/emmo/domain/chemicalsubstance#substance_1e30dcc6_b1c7_4fe9_8f36_1dd427c78a93", + "ZincSymbol": "http://emmo.info/emmo/disciplines/periodictable#EMMO_0bd0c81a-2972-5b2d-8ff5-bb72a82b9c0d", + "ZincTetrafluoroborate": "https://w3id.org/emmo/domain/chemicalsubstance#substance_3297942c_1564_44de_a966_c04fa5da0a4e", + "ZincTriflate": "https://w3id.org/emmo/domain/chemicalsubstance#substance_ec7bf3bb_30b3_4f2c_a12d_9f9f9006a955", + "Zirconium": "https://w3id.org/emmo/domain/chemicalsubstance#substance_55f13456_b4b6_4cf9_998c_8c439b249b3f", + "ZirconiumAtom": "http://emmo.info/emmo/disciplines/periodictable#EMMO_c052baf7-358f-55de-8ca3-9688563c3cfb", + "ZirconiumIVOxide": "https://w3id.org/emmo/domain/chemicalsubstance#substance_371fbcaa_d782_4f4c_86e3_58e1a58d3bea", + "ZirconiumOxideCompound": "https://w3id.org/emmo/domain/chemicalsubstance#substance_a9218f8f_2e80_497e_b968_b4947cf21802", + "ZirconiumSymbol": "http://emmo.info/emmo/disciplines/periodictable#EMMO_7ab01303-b09e-5a90-8a5b-f5087d6559d3", + "comment": "http://emmo.info/emmo#EMMO_c7b62dd7_063a_4c2a_8504_42f7264ba83f", + "conceptualisation": "http://emmo.info/emmo#EMMO_31252f35_c767_4b97_a877_1235076c3e13", + "contact": "http://emmo.info/emmo#EMMO_1246b120_abbe_4840_b0f8_3e4348b24a17", + "dbpediaReference": "http://emmo.info/emmo#EMMO_6dd685dd_1895_46e4_b227_be9f7d643c25", + "definition": "http://emmo.info/emmo#EMMO_70fe84ff_99b6_4206_a9fc_9a8931836d84", + "deprecate_OrganicCompound": "https://w3id.org/emmo/domain/chemicalsubstance#substance_c5c9cf9f_252e_4b28_90f6_56b500db67fc", + "elucidation": "http://emmo.info/emmo#EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9", + "etymology": "http://emmo.info/emmo#EMMO_705f27ae_954c_4f13_98aa_18473fc52b25", + "example": "http://emmo.info/emmo#EMMO_b432d2d5_25f4_4165_99c5_5935a7763c1a", + "figure": "http://emmo.info/emmo#157fdf31_6387_42be_8e72_10530519214a", + "hasAtomicNumber": "http://emmo.info/emmo/disciplines/periodictable#EMMO_a585728e-36c8-5df4-9d95-aa128d2a0e7f", + "hasDataValue": "http://emmo.info/emmo#b6292331_94af_4f00_976b_ea55960c2f1c", + "hasDimensionString": "http://emmo.info/emmo#EMMO_19d925d0_2cf1_40e5_a391_1a99d68409c9", + "hasIUPAC2016AtomicMass": "http://emmo.info/emmo/disciplines/periodictable#EMMO_43de6d01-276c-55ed-a166-ad097ec75575", + "hasNumericalValue": "http://emmo.info/emmo#EMMO_faf79f53_749d_40b2_807c_d34244c192f4", + "hasPrefixMultiplier": "http://emmo.info/emmo#EMMO_95908a5b_2e5e_4a52_9c5d_db25efe76e0f", + "hasPrefixSymbol": "http://emmo.info/emmo#EMMO_d85162ec_6d62_4cdb_a5b9_f092285e5b7f", + "hasSIConversionMultiplier": "http://emmo.info/emmo#EMMO_8189b42e_0995_423a_a26c_51168b27c3cf", + "hasSIConversionOffset": "http://emmo.info/emmo#EMMO_d088a3cb_d3e3_4eb2_9897_00aef0cb00cd", + "hasStringValue": "http://emmo.info/emmo#EMMO_02face50_43a1_40ce_a909_dfe54d5e186b", + "hasSymbolValue": "http://emmo.info/emmo#EMMO_23b579e1_8088_45b5_9975_064014026c42", + "hasURIValue": "http://emmo.info/emmo#EMMO_b35e92d7_7fa0_4661_aa5a_5cea7c8e6925", + "hasURLValue": "http://emmo.info/emmo#EMMO_ac852bf0_3251_4d6b_9e57_acbfcb5e7e08", + "hasURNValue": "http://emmo.info/emmo#EMMO_b7493aee_366c_442d_8f59_49ac7aa664d7", + "iupacReference": "http://emmo.info/emmo#EMMO_fe015383_afb3_44a6_ae86_043628697aa2", + "metrologicalReference": "http://emmo.info/emmo#58e7c821_4af0_4394_89f7_a9649735f4d2", + "molecularFormula": "http://emmo.info/emmo#EMMO_b8c10b72_7cc1_4e82_b4ab_728faf504919", + "omReference": "http://emmo.info/emmo#EMMO_209ba1b3_149f_4ff0_b672_941610eafd72", + "pubChemReference": "http://emmo.info/emmo#EMMO_371f5265_fa29_4081_b722_2c530b1fdddb", + "qudtReference": "http://emmo.info/emmo#EMMO_1f1b164d_ec6a_4faa_8d5e_88bda62316cc", + "test": "http://emmo.info/emmo#EMMO_89b66d76_fa6f_479d_aae3_ea0c5dac2f3e", + "ucumCode": "http://emmo.info/emmo#EMMO_33ae2d07_5526_4555_a0b4_8f4c031b5652", + "uneceCommonCode": "http://emmo.info/emmo#EMMO_0b1cbe60_d380_4787_b92e_be26bdacf2c2", + "unitSymbol": "http://emmo.info/emmo#EMMO_7f1dec83_d85e_4e1b_b7bd_c9442d4f5a64", + "universe": "http://emmo.info/emmo#EMMO_08cb807c_e626_447b_863f_e2835540e918", + "wikidataReference": "http://emmo.info/emmo#EMMO_26bf1bef_d192_4da6_b0eb_d2209698fb54", + "wikipediaReference": "http://emmo.info/emmo#EMMO_c84c6752_6d64_48cc_9500_e54a3c34898d" + } +} diff --git a/sphinx/_static/css/custom.css b/sphinx/_static/css/custom.css index a4e8548..c6d2b5d 100644 --- a/sphinx/_static/css/custom.css +++ b/sphinx/_static/css/custom.css @@ -32,3 +32,8 @@ html[data-theme=dark] table.element-table tr:nth-child(odd) td{ html[data-theme=dark] table.element-table tr:nth-child(even) td{ background-color: black; } +/* this fixes darkmode within the json-ld playground iframe +by inverting all colors if darkmode is active */ +html[data-theme="dark"] iframe[src*="json-ld.org/playground"] { + filter: invert(0.9); +} \ No newline at end of file diff --git a/sphinx/about.rst b/sphinx/about.rst index ca49802..277f8b4 100644 --- a/sphinx/about.rst +++ b/sphinx/about.rst @@ -1,14 +1,9 @@ -.. toctree:: - :hidden: - - example_person_jsonld_nb.ipynb - -About the Battery Ontology +About the Battery Interface Ontology ========================== -The EMMO Battery Domain Ontology is a semantic resource for the terms and relations needed to describe things, processes, and data in the battery domain. It can be used to **generate linked data** for the Semantic Web, **comply with the FAIR data guidelines**, support **interoperaility of data** among different systems, and more! +The Battery Interface Ontology (BattINFO) is a semantic resource for the terms and relations needed to describe things, processes, and data in the battery domain. It can be used to **generate linked data** for the Semantic Web, **comply with the FAIR data guidelines**, support **interoperaility of data** among different systems, and more! -The Battery Ontology is intended to support researchers, engineers, and developers within the electrochemical +BattINFO is intended to support researchers, engineers, and developers within the electrochemical communitiy with activities like: - Incorporating consistent and standardized information into their modeling and simulation activities. @@ -61,7 +56,7 @@ The import structure is summarized in the following table: The onotlogy exists in two forms: (i) the asserted source files and (ii) the pre-inferred version. -The asserted source consists of two files: - ``battery.ttl``: describes terms and object properties for the electrochemistry domain. - ``batteryquantities.ttl``: describes the quantities related to the electrochemistry domain. It is encapsulated to allow it to be imported by other EMMO domains without needing to import the entire ontology. +The asserted source consists of two files: - ``battinfo.ttl``: describes terms and object properties for the battery and electrochemistry domain. ``battinfo-inferred.ttl``: is the pre-inferred version of the ontology. The pre-inferred ontology runs the reasoner on the source files and their imports and complies them into a `pre-inferred ontology file `__. This provides a simpler reference for users of the ontology and removes the barrier of needed to run the reasoner themselves. diff --git a/sphinx/example_linked_data_battery_cell_metadata.ipynb b/sphinx/example_linked_data_battery_cell_metadata.ipynb new file mode 100644 index 0000000..0d4389e --- /dev/null +++ b/sphinx/example_linked_data_battery_cell_metadata.ipynb @@ -0,0 +1,486 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "provenance": [] + }, + "kernelspec": { + "name": "python3", + "display_name": "Python 3" + }, + "language_info": { + "name": "python" + } + }, + "cells": [ + { + "cell_type": "markdown", + "source": [ + "# Example: Simple Battery Cell Metadata\n", + "\n", + "Let's describe an instance of a simple CR2032 coin cell with a capacity defined in a specification sheet from the manufacturer!\n", + "\n", + "This example covers a few topics: \n", + "\n", + "- How to describe a resource using ontology terms and JSON-LD \n", + "- How machines convert JSON-LD into triples \n", + "- What is the meaning of the subject, predicate, and object identifiers \n", + "- How to run a simple query using SPARQL **[Moderate]** \n", + "- How to use the ontology to fetch more information from other sources **[Advanced]** \n", + "\n", + "A live version of this notebook is available on Google Colab [here](https://colab.research.google.com/drive/10F5YRAnO5ubY4Ut3uEjv5rLqvr_GRFC5?usp=sharing)\n" + ], + "metadata": { + "id": "1wseTQGaB4x9" + } + }, + { + "cell_type": "markdown", + "source": [ + "## Describe the powder using ontology terms in JSON-LD format\n", + "The JSON-LD data that we will use is:" + ], + "metadata": { + "id": "jcTVz9-DEh3m" + } + }, + { + "cell_type": "code", + "source": [ + "jsonld = {\n", + " \"@context\": \"https://raw.githubusercontent.com/emmo-repo/domain-battery/master/context.json\",\n", + " \"@type\": \"CR2032\",\n", + " \"schema:name\": \"My CR2032 Coin Cell\",\n", + " \"schema:manufacturer\": {\n", + " \"@id\": \"https://www.wikidata.org/wiki/Q3041255\",\n", + " \"schema:name\": \"SINTEF\"\n", + " },\n", + " \"hasProperty\": {\n", + " \"@type\": [\"NominalCapacity\", \"ConventionalProperty\"],\n", + " \"hasNumericalPart\": {\n", + " \"@type\": \"Real\",\n", + " \"hasNumericalValue\": 230\n", + " },\n", + " \"hasMeasurementUnit\": \"emmo:MilliAmpereHour\"\n", + " }\n", + " }" + ], + "metadata": { + "id": "gohQKEBrF2QP" + }, + "execution_count": 42, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "## Parse this description into a graph\n", + "Now let's see how a machine would process this data by reading it into a Graph!\n", + "\n", + "First, we install and import the python dependencies that we need for this example." + ], + "metadata": { + "id": "in30p-x4H91Y" + } + }, + { + "cell_type": "code", + "source": [ + "# Install and import dependencies\n", + "!pip install jsonschema rdflib requests matplotlib > /dev/null\n", + "\n", + "import json\n", + "import rdflib\n", + "import requests\n", + "import sys\n", + "from IPython.display import Image, display\n", + "import matplotlib.pyplot as plt" + ], + "metadata": { + "id": "wk4sFl_eA2ML" + }, + "execution_count": 43, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "We create the graph using a very handy python package called [rdflib](https://rdflib.readthedocs.io/en/stable/), which provides us a way to parse our json-ld data, run some queries using the language [SPARQL](https://en.wikipedia.org/wiki/SPARQL), and serialize the graph in any RDF compatible format (e.g. JSON-LD, Turtle, etc.)." + ], + "metadata": { + "id": "lotp-0QABV-2" + } + }, + { + "cell_type": "code", + "source": [ + "# Create a new graph\n", + "g = rdflib.Graph()\n", + "\n", + "# Parse our json-ld data into the graph\n", + "g.parse(data=json.dumps(jsonld), format=\"json-ld\")\n", + "\n", + "# Create a SPARQL query to return all the triples in the graph\n", + "query_all = \"\"\"\n", + "SELECT ?subject ?predicate ?object\n", + "WHERE {\n", + " ?subject ?predicate ?object\n", + "}\n", + "\"\"\"\n", + "\n", + "# Execute the SPARQL query\n", + "all_the_things = g.query(query_all)\n", + "\n", + "# Print the results\n", + "for row in all_the_things:\n", + " print(row)\n" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "zWibLw6NIrrq", + "outputId": "6be74891-73f3-43ff-a4d1-29b6697f8b11" + }, + "execution_count": 44, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "(rdflib.term.BNode('N4c3bba051ecb4cb7a8336502c67cf29b'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('file:///content/NominalCapacity'))\n", + "(rdflib.term.BNode('N4c52ea3012a7451c8194bcd5f42b1679'), rdflib.term.URIRef('https://schema.org/manufacturer'), rdflib.term.URIRef('https://www.wikidata.org/wiki/Q3041255'))\n", + "(rdflib.term.BNode('Nc3ad291a291c481481cd4df5c311af50'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_18d180e4_5e3e_42f7_820c_e08951223486'))\n", + "(rdflib.term.BNode('N4c3bba051ecb4cb7a8336502c67cf29b'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_bed1d005_b04e_4a90_94cf_02bc678a8569'), rdflib.term.URIRef('http://emmo.info/emmo#MilliAmpereHour'))\n", + "(rdflib.term.BNode('N4c3bba051ecb4cb7a8336502c67cf29b'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_8ef3cd6d_ae58_4a8d_9fc0_ad8f49015cd0'), rdflib.term.BNode('Nc3ad291a291c481481cd4df5c311af50'))\n", + "(rdflib.term.BNode('N4c52ea3012a7451c8194bcd5f42b1679'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/battery#battery_b61b96ac_f2f4_4b74_82d5_565fe3a2d88b'))\n", + "(rdflib.term.BNode('Nc3ad291a291c481481cd4df5c311af50'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_faf79f53_749d_40b2_807c_d34244c192f4'), rdflib.term.Literal('230', datatype=rdflib.term.URIRef('http://www.w3.org/2001/XMLSchema#integer')))\n", + "(rdflib.term.BNode('N4c52ea3012a7451c8194bcd5f42b1679'), rdflib.term.URIRef('https://schema.org/name'), rdflib.term.Literal('My CR2032 Coin Cell'))\n", + "(rdflib.term.BNode('N4c3bba051ecb4cb7a8336502c67cf29b'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_d8aa8e1f_b650_416d_88a0_5118de945456'))\n", + "(rdflib.term.BNode('N4c52ea3012a7451c8194bcd5f42b1679'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_e1097637_70d2_4895_973f_2396f04fa204'), rdflib.term.BNode('N4c3bba051ecb4cb7a8336502c67cf29b'))\n", + "(rdflib.term.URIRef('https://www.wikidata.org/wiki/Q3041255'), rdflib.term.URIRef('https://schema.org/name'), rdflib.term.Literal('SINTEF'))\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "You can see that our human-readable JSON-LD file has been transformed into some nasty looking (but machine-readable!) triples. Let's look at a couple in more detail to understand what's going on.

\n", + "\n", + "## Examine and explore the triples\n", + "\n", + "Let's start with this one:\n", + "\n", + "|   |   |\n", + "|-----------|--------------------------------------|\n", + "| subject | https://www.wikidata.org/wiki/Q3041255 |\n", + "| predicate | https://schema.org/name |\n", + "| object | ‘SINTEF |\n", + "\n", + "This tells the machine that something with a wikidata identifier has a property called 'name' from the schema.org vocabulary with a literal value '**SINTEF**'. These identifiers serve not only as persistent and unique identifiers for the concepts, but also point to a place where a machine can go to learn more about what it is. Try it yourself! Click on one and see where it takes you!

\n", + "\n", + "\n", + "*Neat, right?!* Let's look at another one:\n", + "\n", + "|   |   |\n", + "|-----------|--------------------------------------|\n", + "| subject | 'Nb9d4bdc220954548a09b8b56f95d9cf3' |\n", + "| predicate | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |\n", + "| object | http://emmo.info/battery#battery_b61b96ac_f2f4_4b74_82d5_565fe3a2d88b |\n", + "\n", + "\n", + "\n", + "This tells the machine that a certain node in the graph is a a type of some thing that exists in the EMMO domain 'battery'. And this gets to one of the difficult bits for humans: many ontologies (like EMMO) use UUIDs for term names to ensure that they are universally unique. It works, but it sacrifices the human readability. Luckily we can get around this by assigning human-readable annotations to that term and/or mapping the IRI to a human readable label in a JSON-LD context like we did above.\n", + "\n", + "Go ahead, click the link and see if you can figure out what this thing is...\n", + "\n", + "...*it's a CR2016!* Now we can see how our simple description in the JSON-LD file has now been converted to a machine-readable IRI.

\n", + "\n", + "## Query the graph using SPARQL [Moderate]\n", + "\n", + "Now, let's write a SPARQL query to get back some specific thing...like what is the name of the manufacturer?" + ], + "metadata": { + "id": "C-w1TbxkI4W5" + } + }, + { + "cell_type": "code", + "source": [ + "query = \"\"\"\n", + "PREFIX schema: \n", + "\n", + "SELECT ?manufacturerName\n", + "WHERE {\n", + " ?thing schema:manufacturer ?manufacturer .\n", + " ?manufacturer schema:name ?manufacturerName .\n", + "}\n", + "\"\"\"\n", + "\n", + "# Execute the SPARQL query\n", + "results = g.query(query)\n", + "\n", + "# Print the results\n", + "for row in results:\n", + " print(row)\n" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "6bXHGG4cI-kr", + "outputId": "5c79fa6e-50a4-4fc2-c513-149bd8cd9170" + }, + "execution_count": 45, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "(rdflib.term.Literal('SINTEF'),)\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "## Fetch additional information from other sources [Advanced]\n", + "Ontologies contain a lot of information about the meaning of things, but they don't always contain an exhaustive list of all the properties. Instead, they often point to other sources where that information exists rather than duplicating it. Let's see how you can use the ontology to fetch additional information from other sources.\n", + "\n", + "First, we parse the ontology into the knowledge graph and retrieve the IRIs for the terms that we are interested in. In this case, we want to retrieve more information about CR2032 from Wikidata, so we query the ontology to find CR2032's Wikidata ID." + ], + "metadata": { + "id": "b7LJC8BubFce" + } + }, + { + "cell_type": "code", + "source": [ + "# Parse the ontology into the knowledge graph\n", + "ontology = \"https://raw.githubusercontent.com/emmo-repo/domain-battery/master/inferred_version/battery-inferred.ttl\"\n", + "g.parse(ontology, format='turtle')\n", + "\n", + "# Fetch the context\n", + "context_url = 'https://raw.githubusercontent.com/emmo-repo/domain-battery/master/context.json'\n", + "response = requests.get(context_url)\n", + "context_data = response.json()\n", + "\n", + "# Look for the IRI of CR2032 in the context\n", + "cr2032_iri = context_data.get('@context', {}).get('CR2032')\n", + "wikidata_iri = context_data.get('@context', {}).get('wikidataReference')\n", + "\n", + "# Query the ontology to find the wikidata id for CR2032\n", + "query = \"\"\"\n", + "SELECT ?wikidataId\n", + "WHERE {\n", + " <%s> <%s> ?wikidataId .\n", + "}\n", + "\"\"\" % (cr2032_iri, wikidata_iri)\n", + "\n", + "qres = g.query(query)\n", + "for row in qres:\n", + " wikidata_id = row.wikidataId.split('/')[-1]\n", + "\n", + "print(f\"The Wikidata ID of CR2032: {wikidata_id}\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "ntT1Rf_yM6sZ", + "outputId": "7eb1b90f-c97e-4d1e-b311-ca9355501c2e" + }, + "execution_count": 46, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "The Wikidata ID of CR2032: Q5013811\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "Now that we have the Wikidata ID for CR2032, we can query their SPARQL endpoint to retrieve some property. Let's ask it for the thickness." + ], + "metadata": { + "id": "XGXFrNa5dKSr" + } + }, + { + "cell_type": "code", + "source": [ + "# Query the Wikidata knowledge graph for more information about zinc\n", + "wikidata_endpoint = \"https://query.wikidata.org/sparql\"\n", + "\n", + "# SPARQL query to get the thickness of a CR2032 cell\n", + "query = \"\"\"\n", + "SELECT ?value ?unit WHERE {\n", + " wd:%s p:P2386 ?statement .\n", + " ?statement ps:P2386 ?value .\n", + " OPTIONAL {\n", + " ?statement psv:P2386 ?valueNode .\n", + " ?valueNode wikibase:quantityUnit ?unit .\n", + " }\n", + "}\n", + "\n", + "\"\"\" % wikidata_id\n", + "\n", + "# Execute the request\n", + "response = requests.get(wikidata_endpoint, params={'query': query, 'format': 'json'})\n", + "data = response.json()\n", + "\n", + "# Extract and print the thickness value\n", + "thickness = data['results']['bindings'][0]['value']['value']\n", + "unit = data['results']['bindings'][0]['unit']['value']\n", + "print(f\"Wikidata says the thickness of a CR2032 cell is: {thickness} {unit}\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "zTBOZAf-dWQQ", + "outputId": "9f9d1c00-d74f-4c76-ceb5-b58b21853c41" + }, + "execution_count": 47, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Wikidata says the thickness of a CR2032 cell is: 20 http://www.wikidata.org/entity/Q174789\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "We can also retrieve more complex data. For example, let's ask Wikidata to show us an image of a CR2032." + ], + "metadata": { + "id": "-xdSIS6Idy5m" + } + }, + { + "cell_type": "code", + "source": [ + "# SPARQL query to get the image of the CR2032 cell (Q758)\n", + "query = \"\"\"\n", + "SELECT ?image WHERE {\n", + " wd:%s wdt:P18 ?image .\n", + "}\n", + "\"\"\" % wikidata_id\n", + "\n", + "# Execute the request\n", + "response = requests.get(wikidata_endpoint, params={'query': query, 'format': 'json'})\n", + "data = response.json()\n", + "\n", + "# Extract and display the image URL\n", + "if data['results']['bindings']:\n", + " image_url = data['results']['bindings'][0]['image']['value']\n", + " print(f\"Image of a CR2032- cell: {image_url}\")\n", + " display(Image(url=image_url, width=300)) # Adjust width and height as needed\n", + "\n", + "else:\n", + " print(\"No image found.\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 339 + }, + "id": "T7bkBY0sNqNY", + "outputId": "c9c3bcf4-d278-4acd-a93b-5a7d553d66fd" + }, + "execution_count": 48, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Image of a CR2032- cell: http://commons.wikimedia.org/wiki/Special:FilePath/CR2032%20battery%2C%20KTS-2728.jpg\n" + ] + }, + { + "output_type": "display_data", + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {} + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "Finally, let's retireve the id for CR2032 in the Google Knowledge Graph and see what it has to say!" + ], + "metadata": { + "id": "mRcFo-MBDVBW" + } + }, + { + "cell_type": "code", + "source": [ + "# SPARQL query to get the Google Knowledge Graph ID of the CR2032 cell\n", + "query = \"\"\"\n", + "SELECT ?id WHERE {\n", + " wd:%s wdt:P2671 ?id .\n", + "}\n", + "\"\"\" % wikidata_id\n", + "\n", + "# Execute the request\n", + "response = requests.get(wikidata_endpoint, params={'query': query, 'format': 'json'})\n", + "data = response.json()\n", + "\n", + "# Extract and display the Google Knowledge Graph ID\n", + "if data['results']['bindings']:\n", + " gkgid = data['results']['bindings'][0]['id']['value']\n", + " gkgns = 'https://www.google.com/search?kgmid='\n", + " gkg = gkgns + gkgid\n", + " print(f\"The Google Knowledge Graph entry for a CR2032 cell: {gkg}\")\n", + "\n", + "else:\n", + " print(\"None found.\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "nAAC5bo8FLD6", + "outputId": "d3543deb-ce22-4d90-f054-6b705c94fb49" + }, + "execution_count": 49, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "The Google Knowledge Graph entry for a CR2032 cell: https://www.google.com/search?kgmid=/g/11bc5qf2g9\n" + ] + } + ] + }, + { + "cell_type": "code", + "source": [], + "metadata": { + "id": "T1qUAeCDVNq3" + }, + "execution_count": 49, + "outputs": [] + } + ] +} \ No newline at end of file diff --git a/sphinx/example_linked_data_custom_battery_cell_metadata.ipynb b/sphinx/example_linked_data_custom_battery_cell_metadata.ipynb new file mode 100644 index 0000000..7388b3d --- /dev/null +++ b/sphinx/example_linked_data_custom_battery_cell_metadata.ipynb @@ -0,0 +1,850 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "provenance": [] + }, + "kernelspec": { + "name": "python3", + "display_name": "Python 3" + }, + "language_info": { + "name": "python" + } + }, + "cells": [ + { + "cell_type": "markdown", + "source": [ + "# Example: Custom Battery Cell Metadata\n", + "\n", + "Let's describe two instances of custom R2032 coin cells with different materials!\n", + "\n", + "This example covers a few topics: \n", + "\n", + "- How to describe a resource using ontology terms and JSON-LD \n", + "- How machines convert JSON-LD into triples \n", + "- How to filter your cells based on some criteria **[Moderate]**\n", + "- How to use the ontology to fetch more information from other sources **[Advanced]** \n", + "\n", + "A live version of this notebook is available on Google Colab [here](https://colab.research.google.com/drive/1k3dGZTz4bDeH4JPToqXsN0svCUkswPDN?usp=sharing)\n" + ], + "metadata": { + "id": "1wseTQGaB4x9" + } + }, + { + "cell_type": "markdown", + "source": [ + "## Describe the powder using ontology terms in JSON-LD format\n", + "The JSON-LD data that we will use is:" + ], + "metadata": { + "id": "jcTVz9-DEh3m" + } + }, + { + "cell_type": "code", + "source": [ + "jsonld_LFPGr = {\n", + " \"@context\": \"https://raw.githubusercontent.com/emmo-repo/domain-battery/master/context.json\",\n", + " \"@type\": \"BatteryCell\",\n", + " \"schema:name\": \"My LFP-Graphite R2032 Coin Cell\",\n", + " \"schema:manufacturer\": {\n", + " \"@id\": \"https://www.wikidata.org/wiki/Q3041255\",\n", + " \"schema:name\": \"SINTEF\"\n", + " },\n", + " \"hasPositiveElectrode\": {\n", + " \"@type\": \"Electrode\",\n", + " \"hasActiveMaterial\": {\n", + " \"@type\": \"LithiumIronPhosphate\"\n", + " }\n", + " },\n", + " \"hasNegativeElectrode\": {\n", + " \"@type\": \"Electrode\",\n", + " \"hasActiveMaterial\": {\n", + " \"@type\": \"Graphite\"\n", + " }\n", + " },\n", + " \"hasCase\": {\n", + " \"@type\": \"R2032\"\n", + " },\n", + " \"hasProperty\": {\n", + " \"@type\": [\"NominalVoltage\", \"ConventionalProperty\"],\n", + " \"hasNumericalPart\": {\n", + " \"@type\": \"Real\",\n", + " \"hasNumericalValue\": 3.2\n", + " },\n", + " \"hasMeasurementUnit\": \"emmo:Volt\"\n", + " }\n", + " }\n", + "\n", + "jsonld_LNOGr = {\n", + " \"@context\": \"https://raw.githubusercontent.com/emmo-repo/domain-battery/master/context.json\",\n", + " \"@type\": \"BatteryCell\",\n", + " \"schema:name\": \"My LNO-Graphite R2032 Coin Cell\",\n", + " \"schema:manufacturer\": {\n", + " \"@id\": \"https://www.wikidata.org/wiki/Q3041255\",\n", + " \"schema:name\": \"SINTEF\"\n", + " },\n", + " \"hasPositiveElectrode\": {\n", + " \"@type\": \"Electrode\",\n", + " \"hasActiveMaterial\": {\n", + " \"@type\": \"LithiumNickelOxide\"\n", + " }\n", + " },\n", + " \"hasNegativeElectrode\": {\n", + " \"@type\": \"Electrode\",\n", + " \"hasActiveMaterial\": {\n", + " \"@type\": \"Graphite\"\n", + " }\n", + " },\n", + " \"hasCase\": {\n", + " \"@type\": \"R2032\"\n", + " },\n", + " \"hasProperty\": {\n", + " \"@type\": [\"NominalVoltage\", \"ConventionalProperty\"],\n", + " \"hasNumericalPart\": {\n", + " \"@type\": \"Real\",\n", + " \"hasNumericalValue\": 3.6\n", + " },\n", + " \"hasMeasurementUnit\": \"emmo:Volt\"\n", + " }\n", + " }" + ], + "metadata": { + "id": "gohQKEBrF2QP" + }, + "execution_count": 48, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "## Parse this description into a graph\n", + "Now let's see how a machine would process this data by reading it into a Graph!\n", + "\n", + "First, we install and import the python dependencies that we need for this example." + ], + "metadata": { + "id": "in30p-x4H91Y" + } + }, + { + "cell_type": "code", + "source": [ + "# Install and import dependencies\n", + "!pip install jsonschema rdflib requests matplotlib > /dev/null\n", + "\n", + "import json\n", + "import rdflib\n", + "import requests\n", + "import sys\n", + "from IPython.display import Image, display\n", + "import matplotlib.pyplot as plt" + ], + "metadata": { + "id": "wk4sFl_eA2ML" + }, + "execution_count": 49, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "We create the graph using a very handy python package called [rdflib](https://rdflib.readthedocs.io/en/stable/), which provides us a way to parse our json-ld data, run some queries using the language [SPARQL](https://en.wikipedia.org/wiki/SPARQL), and serialize the graph in any RDF compatible format (e.g. JSON-LD, Turtle, etc.)." + ], + "metadata": { + "id": "lotp-0QABV-2" + } + }, + { + "cell_type": "code", + "source": [ + "# Create a new graph\n", + "g = rdflib.Graph()\n", + "\n", + "# Parse our json-ld data into the graph\n", + "g.parse(data=json.dumps(jsonld_LFPGr), format=\"json-ld\")\n", + "g.parse(data=json.dumps(jsonld_LNOGr), format=\"json-ld\")\n", + "\n", + "# Create a SPARQL query to return all the triples in the graph\n", + "query_all = \"\"\"\n", + "SELECT ?subject ?predicate ?object\n", + "WHERE {\n", + " ?subject ?predicate ?object\n", + "}\n", + "\"\"\"\n", + "\n", + "# Execute the SPARQL query\n", + "all_the_things = g.query(query_all)\n", + "\n", + "# Print the results\n", + "for row in all_the_things:\n", + " print(row)\n" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "zWibLw6NIrrq", + "outputId": "785ba3d8-9dbc-4b89-df62-931c96bb8216" + }, + "execution_count": 50, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "(rdflib.term.BNode('N1fa58317b5c04a40bdc836b0e29a051d'), rdflib.term.URIRef('https://schema.org/name'), rdflib.term.Literal('My LFP-Graphite R2032 Coin Cell'))\n", + "(rdflib.term.BNode('Na8888f67843f40fa8bc9efe32a39bd02'), rdflib.term.URIRef('http://emmo.info/electrochemistry#electrochemistry_860aa941_5ff9_4452_8a16_7856fad07bee'), rdflib.term.BNode('N1fe8535096ed436e92cc736bb203262f'))\n", + "(rdflib.term.BNode('N8a25bf6bf45743e0bbbd9401567d5dc4'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_bed1d005_b04e_4a90_94cf_02bc678a8569'), rdflib.term.URIRef('http://emmo.info/emmo#Volt'))\n", + "(rdflib.term.BNode('Ne6858b3f64a9483f925ccd464076ab04'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/battery#battery_68ed592a_7924_45d0_a108_94d6275d57f0'))\n", + "(rdflib.term.BNode('Nabed07743a4948009530f6c30a72a556'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_18d180e4_5e3e_42f7_820c_e08951223486'))\n", + "(rdflib.term.BNode('N8a25bf6bf45743e0bbbd9401567d5dc4'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_d8aa8e1f_b650_416d_88a0_5118de945456'))\n", + "(rdflib.term.BNode('N8a25bf6bf45743e0bbbd9401567d5dc4'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_8ef3cd6d_ae58_4a8d_9fc0_ad8f49015cd0'), rdflib.term.BNode('Nabed07743a4948009530f6c30a72a556'))\n", + "(rdflib.term.BNode('Nf303668168c149ee9db9d3c1f077f92f'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/electrochemistry#electrochemistry_639b844a_e801_436b_985d_28926129ead6'))\n", + "(rdflib.term.BNode('Nc84b874ca480485c82214ff777e4d5b0'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('https://w3id.org/emmo/domain/chemicalsubstance#substance_c28a0967_ed23_48cc_a14e_a651d75a19db'))\n", + "(rdflib.term.BNode('N9d60b680f9a548f79d824e66f9f3f3a0'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/electrochemistry#electrochemistry_0f007072-a8dd-4798-b865-1bf9363be627'))\n", + "(rdflib.term.BNode('Ne6858b3f64a9483f925ccd464076ab04'), rdflib.term.URIRef('http://emmo.info/electrochemistry#electrochemistry_5d299271_3f68_494f_ab96_3db9acdd3138'), rdflib.term.BNode('N9d60b680f9a548f79d824e66f9f3f3a0'))\n", + "(rdflib.term.BNode('Ne6858b3f64a9483f925ccd464076ab04'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_e1097637_70d2_4895_973f_2396f04fa204'), rdflib.term.BNode('N8a25bf6bf45743e0bbbd9401567d5dc4'))\n", + "(rdflib.term.BNode('Ndeb892b2acee4a638d8f785513faa6d7'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/electrochemistry#electrochemistry_0f007072-a8dd-4798-b865-1bf9363be627'))\n", + "(rdflib.term.BNode('Ne6858b3f64a9483f925ccd464076ab04'), rdflib.term.URIRef('https://schema.org/name'), rdflib.term.Literal('My LNO-Graphite R2032 Coin Cell'))\n", + 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rdflib.term.URIRef('http://emmo.info/electrochemistry#electrochemistry_860aa941_5ff9_4452_8a16_7856fad07bee'), rdflib.term.BNode('Nc84b874ca480485c82214ff777e4d5b0'))\n", + "(rdflib.term.BNode('N1fa58317b5c04a40bdc836b0e29a051d'), rdflib.term.URIRef('http://emmo.info/electrochemistry#electrochemistry_5d299271_3f68_494f_ab96_3db9acdd3138'), rdflib.term.BNode('N318dda34a11b4390946ce22a6278c83c'))\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "You can see that our human-readable JSON-LD file has been transformed into some nasty looking (but machine-readable!) triples.\n", + "\n", + "## Query the Graph to select instances with certain properties [Advanced]\n", + "\n", + "Now, let's write a SPARQL query to return the names of cells that have a nominal voltage greater than 3.5 V?" + ], + "metadata": { + "id": "C-w1TbxkI4W5" + } + }, + { + "cell_type": "code", + "source": [ + "# Fetch the context\n", + "context_url = 'https://raw.githubusercontent.com/emmo-repo/domain-battery/master/context.json'\n", + "response = requests.get(context_url)\n", + "context_data = response.json()\n", + "\n", + "# Look for the relevant IRIs in the context\n", + "BatteryCell_iri = context_data.get('@context', {}).get('BatteryCell')\n", + "NominalVoltage_iri = context_data.get('@context', {}).get('NominalVoltage')\n", + "hasProperty_iri = context_data.get('@context', {}).get('hasProperty').get('@id')\n", + "hasNumericalPart_iri = context_data.get('@context', {}).get('hasNumericalPart').get('@id')\n", + "hasNumericalValue_iri = context_data.get('@context', {}).get('hasNumericalValue')\n", + "hasMeasurementUnit_iri = context_data.get('@context', {}).get('hasMeasurementUnit').get('@id')\n", + "\n", + "query = f\"\"\"\n", + "PREFIX schema: \n", + "PREFIX emmo: \n", + "\n", + "SELECT ?cellName WHERE {{\n", + " ?cell a <{BatteryCell_iri}>;\n", + " schema:name ?cellName;\n", + " <{hasProperty_iri}> ?property.\n", + "\n", + " ?property a <{NominalVoltage_iri}>;\n", + " <{hasNumericalPart_iri}> ?numericalPart.\n", + "\n", + " ?numericalPart <{hasNumericalValue_iri}> ?voltage.\n", + "\n", + " FILTER (?voltage > 3.5)\n", + "}}\n", + "\"\"\"\n", + "\n", + "# Execute the SPARQL query\n", + "results = g.query(query)\n", + "\n", + "# Print the results\n", + "for row in results:\n", + " print(row)\n" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "6bXHGG4cI-kr", + "outputId": "d74c6a2b-9dc7-4c7f-b5b2-7db4643f310d" + }, + "execution_count": 51, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "(rdflib.term.Literal('My LNO-Graphite R2032 Coin Cell'),)\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "## Fetch additional information from other sources [Advanced]\n", + "\n", + "Ontologies contain a lot of information about the meaning of things, but they don't always contain an exhaustive list of all the properties. Instead, they often point to other sources where that information exists rather than duplicating it. Let's see how you can use the ontology to fetch additional information from other sources." + ], + "metadata": { + "id": "b7LJC8BubFce" + } + }, + { + "cell_type": "code", + "source": [ + "# Parse the ontology into the knowledge graph\n", + "ontology = \"https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/electrochemistry-inferred.ttl\"\n", + "g.parse(ontology, format='turtle')\n", + "\n", + "# Fetch the context\n", + "context_url = 'https://raw.githubusercontent.com/emmo-repo/domain-battery/master/context.json'\n", + "response = requests.get(context_url)\n", + "context_data = response.json()\n", + "\n", + "# Look for the IRI of LithiumNickelOxide in the context\n", + "LithiumNickelOxide_iri = context_data.get('@context', {}).get('LithiumNickelOxide')\n", + "wikidata_iri = context_data.get('@context', {}).get('wikidataReference')\n", + "\n", + "# Query the ontology to find the wikidata id for LithiumNickelOxide\n", + "query = \"\"\"\n", + "SELECT ?wikidataId\n", + "WHERE {\n", + " <%s> <%s> ?wikidataId .\n", + "}\n", + "\"\"\" % (LithiumNickelOxide_iri, wikidata_iri)\n", + "\n", + "qres = g.query(query)\n", + "for row in qres:\n", + " wikidata_id = row.wikidataId.split('/')[-1]\n", + "\n", + "print(f\"The PubChem ID of Lithiun Nickel Oxide is: {wikidata_id}\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "ntT1Rf_yM6sZ", + "outputId": "8945b2dc-8573-4d8e-e1b7-a0d2709569e5" + }, + "execution_count": 52, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "The PubChem ID of Lithiun Nickel Oxide is: Q81988484\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "Finally, let's retireve more information about Lithium Nickel Oxide from Wikidata and PubChem" + ], + "metadata": { + "id": "mRcFo-MBDVBW" + } + }, + { + "cell_type": "code", + "source": [ + "# Query the Wikidata knowledge graph for more information\n", + "wikidata_endpoint = \"https://query.wikidata.org/sparql\"\n", + "\n", + "# SPARQL query to get the PubChem ID\n", + "query = \"\"\"\n", + "SELECT ?id WHERE {\n", + " wd:%s wdt:P662 ?id .\n", + "}\n", + "\"\"\" % wikidata_id\n", + "\n", + "# Execute the request\n", + "response = requests.get(wikidata_endpoint, params={'query': query, 'format': 'json'})\n", + "data = response.json()\n", + "\n", + "# Extract and display the PubChem ID\n", + "if data['results']['bindings']:\n", + " PubChemId = data['results']['bindings'][0]['id']['value']\n", + " print(f\"The PubChem ID for a LithiumNickelOxide cell: {PubChemId}\")\n", + "\n", + "else:\n", + " print(\"None found.\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "nAAC5bo8FLD6", + "outputId": "7bc59e2f-2892-4163-c1fa-d129b96f3433" + }, + "execution_count": 53, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "The PubChem ID for a LithiumNickelOxide cell: 138395181\n" + ] + } + ] + }, + { + "cell_type": "code", + "source": [ + "def get_pubchem_compound_data(cid):\n", + " base_url = \"https://pubchem.ncbi.nlm.nih.gov/rest/pug\"\n", + " compound_url = f\"{base_url}/compound/cid/{cid}/JSON\"\n", + " response = requests.get(compound_url)\n", + " if response.status_code == 200:\n", + " return response.json()\n", + " else:\n", + " return None\n", + "\n", + "# Fetch data for the compound with CID 138395181\n", + "compound_data = get_pubchem_compound_data(PubChemId)\n", + "if compound_data:\n", + " pretty_json = json.dumps(compound_data, indent=4) # Pretty-print the JSON data\n", + " print(pretty_json)\n", + "else:\n", + " print(\"Data not found or error in API request.\")" + ], + "metadata": { + "id": "T1qUAeCDVNq3", + "colab": { + "base_uri": "https://localhost:8080/" + }, + "outputId": "9fabdf0b-adda-4d94-e85c-067efea39029" + }, + "execution_count": 54, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "{\n", + " \"PC_Compounds\": [\n", + " {\n", + " \"id\": {\n", + " \"id\": {\n", + " \"cid\": 138395181\n", + " }\n", + " },\n", + " \"atoms\": {\n", + " \"aid\": [\n", + " 1,\n", + " 2,\n", + " 3,\n", + " 4\n", + " ],\n", + " \"element\": [\n", + " 28,\n", + " 8,\n", + " 8,\n", + " 3\n", + " ],\n", + " \"charge\": [\n", + " {\n", + " \"aid\": 1,\n", + " \"value\": 2\n", + " },\n", + " {\n", + " \"aid\": 2,\n", + " \"value\": -2\n", + " },\n", + " {\n", + " \"aid\": 3,\n", + " \"value\": -2\n", + " },\n", + " {\n", + " \"aid\": 4,\n", + " \"value\": 1\n", + " }\n", + " ]\n", + " },\n", + " \"coords\": [\n", + " {\n", + " \"type\": [\n", + " 1,\n", + " 5,\n", + " 255\n", + " ],\n", + " \"aid\": [\n", + " 1,\n", + " 2,\n", + " 3,\n", + " 4\n", + " ],\n", + " \"conformers\": [\n", + " {\n", + " \"x\": [\n", + " 3.732,\n", + " 2.866,\n", + " 4.5981,\n", + " 2\n", + " ],\n", + " \"y\": [\n", + " 0.25,\n", + " -0.25,\n", + " -0.25,\n", + " 0.25\n", + " ]\n", + " }\n", + " ]\n", + " }\n", + " ],\n", + " \"charge\": -1,\n", + " \"props\": [\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Compound\",\n", + " \"name\": \"Canonicalized\",\n", + " \"datatype\": 5,\n", + " \"release\": \"2019.04.19\"\n", + " },\n", + " \"value\": {\n", + " \"ival\": 1\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Compound Complexity\",\n", + " \"datatype\": 7,\n", + " \"implementation\": \"E_COMPLEXITY\",\n", + " \"version\": \"3.4.6.11\",\n", + " \"software\": \"Cactvs\",\n", + " \"source\": \"xemistry.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"fval\": 0\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Count\",\n", + " \"name\": \"Hydrogen Bond Acceptor\",\n", + " \"datatype\": 5,\n", + " \"implementation\": \"E_NHACCEPTORS\",\n", + " \"version\": \"3.4.6.11\",\n", + " \"software\": \"Cactvs\",\n", + " \"source\": \"xemistry.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"ival\": 2\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Count\",\n", + " \"name\": \"Hydrogen Bond Donor\",\n", + " \"datatype\": 5,\n", + " \"implementation\": \"E_NHDONORS\",\n", + " \"version\": \"3.4.6.11\",\n", + " \"software\": \"Cactvs\",\n", + " \"source\": \"xemistry.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"ival\": 0\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Count\",\n", + " \"name\": \"Rotatable Bond\",\n", + " \"datatype\": 5,\n", + " \"implementation\": \"E_NROTBONDS\",\n", + " \"version\": \"3.4.6.11\",\n", + " \"software\": \"Cactvs\",\n", + " \"source\": \"xemistry.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"ival\": 0\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Fingerprint\",\n", + " \"name\": \"SubStructure Keys\",\n", + " \"datatype\": 16,\n", + " \"parameters\": \"extended 2\",\n", + " \"implementation\": \"E_SCREEN\",\n", + " \"version\": \"3.4.6.11\",\n", + " \"software\": \"Cactvs\",\n", + " \"source\": \"xemistry.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"binary\": \"00000371080030000000000800000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"IUPAC Name\",\n", + " \"name\": \"Allowed\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.6.6\",\n", + " \"software\": \"LexiChem\",\n", + " \"source\": \"openeye.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"lithium;nickelous;oxygen(2-)\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"IUPAC Name\",\n", + " \"name\": \"CAS-like Style\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.6.6\",\n", + " \"software\": \"LexiChem\",\n", + " \"source\": \"openeye.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"lithium;nickel(2+);oxygen(2-)\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"IUPAC Name\",\n", + " \"name\": \"Markup\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.6.6\",\n", + " \"software\": \"LexiChem\",\n", + " \"source\": \"openeye.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"lithium;nickel(2+);oxygen(2-)\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"IUPAC Name\",\n", + " \"name\": \"Preferred\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.6.6\",\n", + " \"software\": \"LexiChem\",\n", + " \"source\": \"openeye.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"lithium;nickel(2+);oxygen(2-)\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"IUPAC Name\",\n", + " \"name\": \"Systematic\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.6.6\",\n", + " \"software\": \"LexiChem\",\n", + " \"source\": \"openeye.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"lithium;nickel(2+);oxygen(2-)\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"IUPAC Name\",\n", + " \"name\": \"Traditional\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.6.6\",\n", + " \"software\": \"LexiChem\",\n", + " \"source\": \"openeye.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"lithium;nickelous;oxygen(2-)\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"InChI\",\n", + " \"name\": \"Standard\",\n", + " \"datatype\": 1,\n", + " \"version\": \"1.0.5\",\n", + " \"software\": \"InChI\",\n", + " \"source\": \"iupac.org\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"InChI=1S/Li.Ni.2O/q+1;+2;2*-2\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"InChIKey\",\n", + " \"name\": \"Standard\",\n", + " \"datatype\": 1,\n", + " \"version\": \"1.0.5\",\n", + " \"software\": \"InChI\",\n", + " \"source\": \"iupac.org\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"FDVOICKSQXHDAQ-UHFFFAOYSA-N\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Mass\",\n", + " \"name\": \"Exact\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.1\",\n", + " \"software\": \"PubChem\",\n", + " \"source\": \"ncbi.nlm.nih.gov\",\n", + " \"release\": \"2021.05.07\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"96.941174\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Molecular Formula\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.1\",\n", + " \"software\": \"PubChem\",\n", + " \"source\": \"ncbi.nlm.nih.gov\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"LiNiO2-\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Molecular Weight\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.1\",\n", + " \"software\": \"PubChem\",\n", + " \"source\": \"ncbi.nlm.nih.gov\",\n", + " \"release\": \"2021.05.07\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"97.7\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"SMILES\",\n", + " \"name\": \"Canonical\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.1.5\",\n", + " \"software\": \"OEChem\",\n", + " \"source\": \"openeye.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"[Li+].[O-2].[O-2].[Ni+2]\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"SMILES\",\n", + " \"name\": \"Isomeric\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.1.5\",\n", + " \"software\": \"OEChem\",\n", + " \"source\": \"openeye.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"[Li+].[O-2].[O-2].[Ni+2]\"\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Topological\",\n", + " \"name\": \"Polar Surface Area\",\n", + " \"datatype\": 7,\n", + " \"implementation\": \"E_TPSA\",\n", + " \"version\": \"3.4.6.11\",\n", + " \"software\": \"Cactvs\",\n", + " \"source\": \"xemistry.com\",\n", + " \"release\": \"2019.06.18\"\n", + " },\n", + " \"value\": {\n", + " \"fval\": 2\n", + " }\n", + " },\n", + " {\n", + " \"urn\": {\n", + " \"label\": \"Weight\",\n", + " \"name\": \"MonoIsotopic\",\n", + " \"datatype\": 1,\n", + " \"version\": \"2.1\",\n", + " \"software\": \"PubChem\",\n", + " \"source\": \"ncbi.nlm.nih.gov\",\n", + " \"release\": \"2021.05.07\"\n", + " },\n", + " \"value\": {\n", + " \"sval\": \"96.941174\"\n", + " }\n", + " }\n", + " ],\n", + " \"count\": {\n", + " \"heavy_atom\": 4,\n", + " \"atom_chiral\": 0,\n", + " \"atom_chiral_def\": 0,\n", + " \"atom_chiral_undef\": 0,\n", + " \"bond_chiral\": 0,\n", + " \"bond_chiral_def\": 0,\n", + " \"bond_chiral_undef\": 0,\n", + " \"isotope_atom\": 0,\n", + " \"covalent_unit\": 4,\n", + " \"tautomers\": -1\n", + " }\n", + " }\n", + " ]\n", + "}\n" + ] + } + ] + } + ] +} \ No newline at end of file diff --git a/sphinx/example_linked_data_zinc_powder.ipynb b/sphinx/example_linked_data_zinc_powder.ipynb new file mode 100644 index 0000000..9b8fe83 --- /dev/null +++ b/sphinx/example_linked_data_zinc_powder.ipynb @@ -0,0 +1,435 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "provenance": [] + }, + "kernelspec": { + "name": "python3", + "display_name": "Python 3" + }, + "language_info": { + "name": "python" + } + }, + "cells": [ + { + "cell_type": "markdown", + "source": [ + "# Example: Zinc Powder from a Supplier\n", + "\n", + "Let's describe an instance of some zinc powder with a set of properties defined in the specification sheet from the manufacturer!\n", + "\n", + "This example covers a few topics: \n", + "\n", + "- How to describe a resource using ontology terms and JSON-LD \n", + "- How machines convert JSON-LD into triples \n", + "- What is the meaning of the subject, predicate, and object identifiers \n", + "- How to run a simple query using SPARQL **[Moderate]** \n", + "- How to use the ontology to fetch more information from other sources **[Advanced]** \n", + "\n", + "A live version of this notebook is available on Google Colab [here](https://colab.research.google.com/drive/19PxdZDPcKda8Ji6Nyzsz-_8KJFgNkmCa?usp=sharing)\n" + ], + "metadata": { + "id": "1wseTQGaB4x9" + } + }, + { + "cell_type": "markdown", + "source": [ + "## Describe the powder using ontology terms in JSON-LD format\n", + "The JSON-LD data that we will use is:" + ], + "metadata": { + "id": "jcTVz9-DEh3m" + } + }, + { + "cell_type": "code", + "source": [ + "jsonld = {\n", + " \"@context\": \"https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/context.json\",\n", + " \"@type\": [\"Zinc\", \"Powder\"],\n", + " \"schema:manufacturer\": {\n", + " \"@id\": \"https://www.wikidata.org/wiki/Q680841\",\n", + " \"schema:name\": \"Sigma-Aldrich\"\n", + " },\n", + " \"schema:productID\": \"324930\",\n", + " \"schema:url\": \"https://www.sigmaaldrich.com/NO/en/product/aldrich/324930\",\n", + " \"hasProperty\": [\n", + " {\n", + " \"@type\": [\"D95ParticleSize\", \"ConventionalProperty\"],\n", + " \"hasNumericalPart\": {\n", + " \"@type\": \"Real\",\n", + " \"hasNumericalValue\": 150\n", + " },\n", + " \"hasMeasurementUnit\": \"emmo:MicroMetre\",\n", + " \"dc:source\": \"https://www.sigmaaldrich.com/NO/en/product/aldrich/324930\"\n", + " }\n", + " ]\n", + "}" + ], + "metadata": { + "id": "gohQKEBrF2QP" + }, + "execution_count": 104, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "## Parse this description into a graph\n", + "Now let's see how a machine would process this data by reading it into a Graph!\n", + "\n", + "First, we install and import the python dependencies that we need for this example." + ], + "metadata": { + "id": "in30p-x4H91Y" + } + }, + { + "cell_type": "code", + "source": [ + "# Install and import dependencies\n", + "!pip install jsonschema rdflib requests matplotlib > /dev/null\n", + "\n", + "import json\n", + "import rdflib\n", + "import requests\n", + "import sys\n", + "from IPython.display import Image, display\n", + "import matplotlib.pyplot as plt" + ], + "metadata": { + "id": "wk4sFl_eA2ML" + }, + "execution_count": 105, + "outputs": [] + }, + { + "cell_type": "markdown", + "source": [ + "We create the graph using a very handy python package called [rdflib](https://rdflib.readthedocs.io/en/stable/), which provides us a way to parse our json-ld data, run some queries using the language [SPARQL](https://en.wikipedia.org/wiki/SPARQL), and serialize the graph in any RDF compatible format (e.g. JSON-LD, Turtle, etc.)." + ], + "metadata": { + "id": "lotp-0QABV-2" + } + }, + { + "cell_type": "code", + "source": [ + "# Create a new graph\n", + "g = rdflib.Graph()\n", + "\n", + "# Parse our json-ld data into the graph\n", + "g.parse(data=json.dumps(jsonld), format=\"json-ld\")\n", + "\n", + "# Create a SPARQL query to return all the triples in the graph\n", + "query_all = \"\"\"\n", + "SELECT ?subject ?predicate ?object\n", + "WHERE {\n", + " ?subject ?predicate ?object\n", + "}\n", + "\"\"\"\n", + "\n", + "# Execute the SPARQL query\n", + "all_the_things = g.query(query_all)\n", + "\n", + "# Print the results\n", + "for row in all_the_things:\n", + " print(row)\n" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "zWibLw6NIrrq", + "outputId": "2b87d0a0-06b4-4093-f44b-4add7f9651e0" + }, + "execution_count": 106, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "(rdflib.term.BNode('Nba3653d5211a479faa84120717afec04'), rdflib.term.URIRef('https://schema.org/manufacturer'), rdflib.term.URIRef('https://www.wikidata.org/wiki/Q680841'))\n", + "(rdflib.term.BNode('Nbad48dcf37014f5989126dde499c31e7'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_d8aa8e1f_b650_416d_88a0_5118de945456'))\n", + "(rdflib.term.BNode('Nba17008e342643b8848eb653b0cc6c5f'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_18d180e4_5e3e_42f7_820c_e08951223486'))\n", + "(rdflib.term.URIRef('https://www.wikidata.org/wiki/Q680841'), rdflib.term.URIRef('https://schema.org/name'), rdflib.term.Literal('Sigma-Aldrich'))\n", + "(rdflib.term.BNode('Nbad48dcf37014f5989126dde499c31e7'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('https://w3id.org/emmo/domain/electrochemistry#electrochemistry_02d2d1d1_241c_429b_b4e7_31f2c3dc4835'))\n", + "(rdflib.term.BNode('Nbad48dcf37014f5989126dde499c31e7'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_bed1d005_b04e_4a90_94cf_02bc678a8569'), rdflib.term.URIRef('http://emmo.info/emmo#MicroMetre'))\n", + "(rdflib.term.BNode('Nba3653d5211a479faa84120717afec04'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('https://w3id.org/emmo/domain/electrochemistry#electrochemistry_ee479886_6805_4018_95e1_500185e44215'))\n", + "(rdflib.term.BNode('Nba3653d5211a479faa84120717afec04'), rdflib.term.URIRef('https://schema.org/url'), rdflib.term.Literal('https://www.sigmaaldrich.com/NO/en/product/aldrich/324930'))\n", + "(rdflib.term.BNode('Nbad48dcf37014f5989126dde499c31e7'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_8ef3cd6d_ae58_4a8d_9fc0_ad8f49015cd0'), rdflib.term.BNode('Nba17008e342643b8848eb653b0cc6c5f'))\n", + "(rdflib.term.BNode('Nba3653d5211a479faa84120717afec04'), rdflib.term.URIRef('https://schema.org/productID'), rdflib.term.Literal('324930'))\n", + "(rdflib.term.BNode('Nba3653d5211a479faa84120717afec04'), rdflib.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.term.URIRef('https://w3id.org/emmo/domain/chemicalsubstance#substance_9bd78e1c_a4dc_41b6_8013_adb51df1ffdc'))\n", + "(rdflib.term.BNode('Nba17008e342643b8848eb653b0cc6c5f'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_faf79f53_749d_40b2_807c_d34244c192f4'), rdflib.term.Literal('150', datatype=rdflib.term.URIRef('http://www.w3.org/2001/XMLSchema#integer')))\n", + "(rdflib.term.BNode('Nbad48dcf37014f5989126dde499c31e7'), rdflib.term.URIRef('http://purl.org/dc/elements/1.1/source'), rdflib.term.Literal('https://www.sigmaaldrich.com/NO/en/product/aldrich/324930'))\n", + "(rdflib.term.BNode('Nba3653d5211a479faa84120717afec04'), rdflib.term.URIRef('http://emmo.info/emmo#EMMO_e1097637_70d2_4895_973f_2396f04fa204'), rdflib.term.BNode('Nbad48dcf37014f5989126dde499c31e7'))\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "You can see that our human-readable JSON-LD file has been transformed into some nasty looking (but machine-readable!) triples. Let's look at a couple in more detail to understand what's going on.

\n", + "\n", + "## Examine and explore the triples\n", + "\n", + "Let's start with this one:\n", + "\n", + "|   |   |\n", + "|-----------|--------------------------------------|\n", + "| subject | https://www.wikidata.org/wiki/Q680841 |\n", + "| predicate | https://schema.org/name |\n", + "| object | ‘Sigma-Aldrich’ |\n", + "\n", + "This tells the machine that something with a wikidata identifier has a property called 'name' from the schema.org vocabulary with a literal value '**Sigma-Aldrich**'. These identifiers serve not only as persistent and unique identifiers for the concepts, but also point to a place where a machine can go to learn more about what it is. Try it yourself! Click on one and see where it takes you!

\n", + "\n", + "\n", + "*Neat, right?!* Let's look at another one:\n", + "\n", + "|   |   |\n", + "|-----------|--------------------------------------|\n", + "| subject | 'Nb9d4bdc220954548a09b8b56f95d9cf3' |\n", + "| predicate | http://www.w3.org/1999/02/22-rdf-syntax-ns#type |\n", + "| object | https://w3id.org/emmo/domain/chemicalsubstance#substance_9bd78e1c_a4dc_41b6_8013_adb51df1ffdc |\n", + "\n", + "\n", + "\n", + "This tells the machine that a certain node in the graph is a a type of some thing that exists in the EMMO domain 'chemicalsubstance'. And this gets to one of the difficult bits for humans: many ontologies (like EMMO) use UUIDs for term names to ensure that they are universally unique. It works, but it sacrifices the human readability. Luckily we can get around this by assigning human-readable annotations to that term and/or mapping the IRI to a human readable label in a JSON-LD context like we did above.\n", + "\n", + "Go ahead, click the link and see if you can figure out what this thing is...\n", + "\n", + "...*it's Zinc!* Now we can see how our simple description in the JSON-LD file has now been converted to a machine-readable IRI.

\n", + "\n", + "## Query the graph using SPARQL [Moderate]\n", + "\n", + "Now, let's write a SPARQL query to get back some specific thing...like what is the name of the manufacturer?" + ], + "metadata": { + "id": "C-w1TbxkI4W5" + } + }, + { + "cell_type": "code", + "source": [ + "query = \"\"\"\n", + "PREFIX schema: \n", + "\n", + "SELECT ?manufacturerName\n", + "WHERE {\n", + " ?thing schema:manufacturer ?manufacturer .\n", + " ?manufacturer schema:name ?manufacturerName .\n", + "}\n", + "\"\"\"\n", + "\n", + "# Execute the SPARQL query\n", + "results = g.query(query)\n", + "\n", + "# Print the results\n", + "for row in results:\n", + " print(row)\n" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "6bXHGG4cI-kr", + "outputId": "c1a5fef2-f4bc-4e63-dc87-617f6bb9cecd" + }, + "execution_count": 107, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "(rdflib.term.Literal('Sigma-Aldrich'),)\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "## Fetch additional information from other sources [Advanced]\n", + "Ontologies contain a lot of information about the meaning of things, but they don't always contain an exhaustive list of all the properties. Instead, they often point to other sources where that information exists rather than duplicating it. Let's see how you can use the ontology to fetch additional information from other sources.\n", + "\n", + "First, we parse the ontology into the knowledge graph and retrieve the IRIs for the terms that we are interested in. In this case, we want to retrieve more information about Zinc from Wikidata, so we query the ontology to find Zinc's Wikidata ID." + ], + "metadata": { + "id": "b7LJC8BubFce" + } + }, + { + "cell_type": "code", + "source": [ + "# Parse the ontology into the knowledge graph\n", + "ontology = \"https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/electrochemistry-inferred.ttl\"\n", + "g.parse(ontology, format='turtle')\n", + "\n", + "# Fetch the context\n", + "context_url = 'https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/context.json'\n", + "response = requests.get(context_url)\n", + "context_data = response.json()\n", + "\n", + "# Look for the IRI of Zinc in the context\n", + "zinc_iri = context_data.get('@context', {}).get('Zinc')\n", + "wikidata_iri = context_data.get('@context', {}).get('wikidataReference')\n", + "\n", + "# Query the ontology to find the wikidata id for zinc\n", + "query = \"\"\"\n", + "SELECT ?wikidataId\n", + "WHERE {\n", + " <%s> <%s> ?wikidataId .\n", + "}\n", + "\"\"\" % (zinc_iri, wikidata_iri)\n", + "\n", + "qres = g.query(query)\n", + "for row in qres:\n", + " wikidata_id = row.wikidataId.split('/')[-1]\n", + "\n", + "print(f\"The Wikidata ID of Zinc: {wikidata_id}\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "ntT1Rf_yM6sZ", + "outputId": "dbd2e4a6-6a4e-4e85-f221-ee240e79c9af" + }, + "execution_count": 108, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "The Wikidata ID of Zinc: Q758\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "Now that we have the Wikidata ID for Zinc, we can query their SPARQL endpoint to retrieve some property. Let's ask it for the atomic mass." + ], + "metadata": { + "id": "XGXFrNa5dKSr" + } + }, + { + "cell_type": "code", + "source": [ + "# Query the Wikidata knowledge graph for more information about zinc\n", + "wikidata_endpoint = \"https://query.wikidata.org/sparql\"\n", + "\n", + "# SPARQL query to get the atomic mass of zinc (Q758)\n", + "query = \"\"\"\n", + "SELECT ?mass WHERE {\n", + " wd:%s wdt:P2067 ?mass .\n", + "}\n", + "\"\"\" % wikidata_id\n", + "\n", + "# Execute the request\n", + "response = requests.get(wikidata_endpoint, params={'query': query, 'format': 'json'})\n", + "data = response.json()\n", + "\n", + "# Extract and print the mass value\n", + "mass = data['results']['bindings'][0]['mass']['value']\n", + "print(f\"Wikidata says the atomic mass of zinc is: {mass}\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "zTBOZAf-dWQQ", + "outputId": "e894b2c6-e2fc-4564-b77f-3e623afeecdb" + }, + "execution_count": 109, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Wikidata says the atomic mass of zinc is: 65.38\n" + ] + } + ] + }, + { + "cell_type": "markdown", + "source": [ + "We can also retrieve more complex data. For example, let's ask Wikidata to show us an image of zinc." + ], + "metadata": { + "id": "-xdSIS6Idy5m" + } + }, + { + "cell_type": "code", + "source": [ + "# SPARQL query to get the image of zinc (Q758)\n", + "query = \"\"\"\n", + "SELECT ?image WHERE {\n", + " wd:%s wdt:P18 ?image .\n", + "}\n", + "\"\"\" % wikidata_id\n", + "\n", + "# Execute the request\n", + "response = requests.get(wikidata_endpoint, params={'query': query, 'format': 'json'})\n", + "data = response.json()\n", + "\n", + "# Extract and display the image URL\n", + "if data['results']['bindings']:\n", + " image_url = data['results']['bindings'][0]['image']['value']\n", + " print(f\"Image of Zinc: {image_url}\")\n", + " display(Image(url=image_url, width=300)) # Adjust width and height as needed\n", + "\n", + "else:\n", + " print(\"No image found for Zinc.\")" + ], + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 222 + }, + "id": "T7bkBY0sNqNY", + "outputId": "a5cad6b9-84be-43b2-9411-569f938a09fc" + }, + "execution_count": 110, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Image of Zinc: http://commons.wikimedia.org/wiki/Special:FilePath/Zinc%20fragment%20sublimed%20and%201cm3%20cube.jpg\n" + ] + }, + { + "output_type": "display_data", + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {} + } + ] + }, + { + "cell_type": "code", + "source": [], + "metadata": { + "id": "T1qUAeCDVNq3" + }, + "execution_count": 110, + "outputs": [] + } + ] +} \ No newline at end of file diff --git a/sphinx/examples.rst b/sphinx/examples.rst index ebdea2e..5e9d16c 100644 --- a/sphinx/examples.rst +++ b/sphinx/examples.rst @@ -1,3 +1,10 @@ +.. toctree:: + :hidden: + + example_linked_data_battery_cell_metadata.ipynb + example_linked_data_custom_battery_cell_metadata.ipynb + example_linked_data_zinc_powder.ipynb + Examples ======== @@ -6,7 +13,21 @@ Here are some examples to help you get started. You are free to re-use or modify .. grid:: .. grid-item-card:: - :link: example_zinc_powder.html + :link: example_linked_data_battery_cell_metadata.html + + :octicon:`diff;1em;sd-text-info` Simple Battery Cell Metadata + ^^^^^^^^^^^ + Metadata for a simple CR2032 coin cell. Also includes exercises for understanding Linked Data basics and fetching additional information from the Wikidata knowledge graph. + + .. grid-item-card:: + :link: example_linked_data_custom_battery_cell_metadata.html + + :octicon:`diff;1em;sd-text-info` Custom Battery Cell Metadata + ^^^^^^^^^^^ + Metadata for custom R2032 coin cells with different materials. Also includes exercises for filtering data from the graph and querying the PubChem API. + + .. grid-item-card:: + :link: example_linked_data_zinc_powder.html :octicon:`ruby;1em;sd-text-info` Zinc Powder ^^^^^^^^^^^ diff --git a/sphinx/getstarted.rst b/sphinx/getstarted.rst index ae27d56..eff26af 100644 --- a/sphinx/getstarted.rst +++ b/sphinx/getstarted.rst @@ -15,9 +15,9 @@ Step 2: Download the pre-inferred version of the ontology Ontologies within the EMMO universe import many different modules to try to re-use knowledge and terms from other domains. We then run a tool called a "reasoner" to make logical inferrences about how terms from different domains are connected, and lump them into one ontology. -We make it easy for you by providing a pre-inferred version in advance. You can `download it from the GitHub repository `__ or access it at anytime using this URL: +We make it easy for you by providing a pre-inferred version in advance. You can `download it from the GitHub repository `__ or access it at anytime using this URL: -https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/electrochemistry-inferred.ttl +https://raw.githubusercontent.com/BIG-MAP/BattINFO/master/battinfo-inferred.ttl Step 3: Open and explore the ontology file in Protégé ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/sphinx/index.rst b/sphinx/index.rst index 75f978e..25ba0a8 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -22,16 +22,20 @@ Welcome to the **Battery Interface Ontology (BattINFO)**, a semantic resource wi :linenos: { - "@context": "https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/context.json", - "@type": "ElectrochemicalCell", - "hasNegativeElectrode": { - "@type": "ZincElectrode" + "@context": "https://raw.githubusercontent.com/emmo-repo/domain-battery/master/context.json", + "@type": "CR2032", + "schema:name": "My CR2032 Coin Cell", + "schema:manufacturer": { + "@id": "https://www.wikidata.org/wiki/Q3041255", + "schema:name": "SINTEF" }, - "hasPositiveElectrode": { - "@type": "ManganeseDioxideElectrode" - }, - "hasElectrolyte": { - "@type": "AlkalineElectrolyte" + "hasProperty": { + "@type": ["NominalCapacity", "ConventionalProperty"], + "hasNumericalPart": { + "@type": "Real", + "hasNumericalValue": 230 + }, + "hasMeasurementUnit": "emmo:MilliAmpereHour" } } @@ -40,7 +44,7 @@ Welcome to the **Battery Interface Ontology (BattINFO)**, a semantic resource wi .. raw:: html
- +