diff --git a/examples/AI4Green/Export workbook-2024-08-27-export.eln b/examples/AI4Green/Export workbook-2024-08-27-export.eln new file mode 100644 index 0000000..ed60fb5 Binary files /dev/null and b/examples/AI4Green/Export workbook-2024-08-27-export.eln differ diff --git a/examples/AI4Green/README.md b/examples/AI4Green/README.md new file mode 100644 index 0000000..1c6fd7a --- /dev/null +++ b/examples/AI4Green/README.md @@ -0,0 +1,173 @@ +# AI4Green + +## Information + +* Repo: https://github.com/AI4Green/AI4Green +* Website: https://ai4green.app/ + +### Structure of the AI4Green example + +This AI4Green export is for a single reaction + +Key parts of the reaction dataset are: +- The text field which renders the summary table in HTML +- Automatically generated .RDF (reaction data file) attachment and any additional file attachments + +## Concepts used + +Here is a correspondance between concepts in AI4Green and how they are translated in the metadata json file in the archive: + +| AI4Green concepts | JSON property | +|----------------------------|----------------| +| summary_table | text || +| comment | comment | +| description (experimental) | description | +| mimetype | encodingFormat | +| time_of_creation | dateCreated || +| time_of_update | dateModified | +| author | author || +| name | name | + + +### export.eln +```json +{ + "@context": "https://w3id.org/ro/crate/1.1/context", + "@graph": [ + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": { + "@id": "https://w3id.org/ro/crate/1.1" + }, + "schemaVersion": "1.0", + "dateCreated": "2024-08-27 11:01:48", + "parentOrganization": { + "@id": "#university-of-nottingham", + "@type": "Organization", + "name": "University of Nottingham", + "logo": "https://www.nottingham.ac.uk/Brand/LegacyAssets/images-multimedia/2022/Logos/BrandEvolution-NottinghamBlue-Cropped-450x173.png", + "url": "https://www.nottingham.ac.uk/" + }, + "sdPublisher": { + "@type": "Organization", + "name": "AI4Green", + "slogan": "AI for Green Chemistry. Electronic Lab Notebook with Machine Learning Support.", + "url": "https://www.ai4green.app", + "parentOrganization": "#university-of-nottingham" + }, + "version": "1.0" + }, + { + "@id": "#ro-crate_created", + "@type": "CreateAction", + "object": { + "@id": "./" + }, + "name": "RO-Crate created", + "endTime": "2024-08-27 11:01:48", + "instrument": { + "@id": "https://www.ai4green.app", + "@type": "SoftwareApplication", + "name": "AI4Green", + "version": "1.6.0", + "git_commit_hash": "b6e1157", + "identifier": "https://www.ai4green.app" + }, + "actionStatus": { + "@id": "http://schema.org/CompletedActionStatus" + } + }, + { + "@id": "./", + "@type": [ + "Dataset" + ], + "hasPart": [ + { + "@id": "./AI4-001/" + } + ] + }, + { + "@id": "./AI4-001/", + "@type": "Dataset", + "name": "Amidation", + "author": { + "@id": "./author/7" + }, + "dateCreated": "2024-07-18 15:56:12", + "dateModified": "2024-07-18 16:05:51", + "comment": [ + { + "@id": "comment-id/AI4-001/5" + } + ], + "hasPart": [ + { + "@id": "./AI4-001/AI4-001.rxn" + }, + { + "@id": "./AI4-001/AI4-001.json" + }, + { + "@id": "./AI4-001/AI4-001-summary.pdf" + } + ], + "description": "Benzoic acid, ethylamine, diisopropylamine and HATU were mixed at RT for 2 hours. The reaction mixture was washed with aqueous sodium chloride and extracted in ethyl acetate. The resultant mixture was concentrated under vacuum and purified by silica gel, eluting at 70% ethyl acetate 30% cyclohexane. This yielded an off-white solid (100 mg, 82%). ", + "text": "

AI4-001

Reaction Smiles: OC(=O)C1=CC=CC=C1.CCN>>CCNC(=O)C1=CC=CC=C1
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
№Reactants/catalysts/reagentsMol.WtDensity (g/mL)Conc. (M)Equiv.Amount (mmol)Volume (mL)Mass (mg)
1Benzoic Acid122.1210.820.00100
2Ethylamine45.0821.640.0073.8
3Diisopropylamine101.190.7171.41.150.16116
4O-(7-Azabenzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate380.231.20.980.00374
SolventsVolume (mL)
5Dimethylformamide1
ProductMol.WtTheoretical Yield (mg)Unreacted (mg)Product Mass (mg)% Yield
6N-Ethylbenzamide149.19122510081.86
HazardsHazard RatingExposure PotentialRisk Rating
1H315 Causes skin irritation, H318 Causes serious eye damage, H372 Causes damage to organs through prolonged or repeated exposureVHLH
2H220 Extremely flammable gas, H319 Causes serious eye irritation, H335 May cause respiratory irritationHHH
3H225 Highly Flammable liquid and vapor, H302 Harmful if swallowed, H314 Causes severe skin burns and eye damage, H332 Harmful if inhaledHMH
4H228 Flammable solid, H315 Causes skin irritation, H317 May cause an allergic skin reaction, H319 Causes serious eye irritation, H335 May cause respiratory irritationVHLH
5H226 Flammable liquid and vapor, H312 Harmful in contact with skin, H319 Causes serious eye irritation, H332 Harmful if inhaled, H360D May damage the unborn childVHLH
6H302 Harmful if swallowedMLL
Risk Rating:VH
Sustainability (CHEM21)
\n\n\n\n\n\n\n\n
Solvents
Dimethylformamide
\n		\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
SafetyTemp ℃\n\nElements \n\nBatch/flowIsolationStoichiometryCat. Recovery
VH20
Atom EfficiencyMass EfficiencyYieldConversionSelectivity
23.01581.869586
\n
Standard Protocols:
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Disposal of Waste Materials:
Spillage Procedure:
\n
\nOther Risks, controls, containment, location and PPE.
\n (Hazardous by Products. Exothermic reactions. The need to inform others of risks. Lab and hood number.)
Hazard categorisation given GLP and other controls\n specified
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Hazard
Potential to cause harm		\n\n
\n\n
\n\n		Risk Category (A-D)
\n
\n		Risk Score HxRxC
Risk
Likelihood of exposure		\n\n
\n\n
\n\n
\n		4
Consequences
Who will be affected		\n\n
\n\n
\n\n\n		\n
\n
\n
Signed:

Researcher:Joe DaviesSupervisor:Super Joe Davies
\n
\n
", + "encodingFormat": "text/html", + "url": "https://www.ai4green.app/Development-Workgroup/Export%20workbook/AI4-001/no" + }, + { + "@id": "./AI4-001/AI4-001.rxn", + "@type": "File", + "name": "AI4-001.rxn", + "description": "A Chemistry specific format with molecules represented in a Chemical Table format and assigned as reactants, products, or agents", + "encodingFormat": "chemical/x-mdl-rxn", + "contentSize": "5462", + "sha256": "62d571bac873051fee6cc8ee5f1c82d0ede91485ec65f5778aceba2fdb889bd5", + "dateModified": "2024-08-27 11:01:48" + }, + { + "@id": "./AI4-001/AI4-001.json", + "@type": "File", + "name": "AI4-001.json", + "description": "A structured data format commonly used for exchanging information between servers and web applications. Keys and values are used to describe reaction metadata", + "encodingFormat": "application/json", + "contentSize": "3130", + "sha256": "76b8252281b387d436d198a828e2e6e3d3e24d44d76164ac65f545f2ab83d873", + "dateModified": "2024-08-27 11:01:48" + }, + { + "@id": "./AI4-001/AI4-001-summary.pdf", + "@type": "File", + "name": "AI4-001-summary.pdf", + "description": "Reaction data uploaded by user", + "encodingFormat": "application/pdf", + "contentSize": "853054", + "sha256": "2d08aa4e44fd2ad86dbb30e48ace404c4b621e0571bc57f36deb6ccf071ed897", + "dateModified": "2024-07-18T16:05:59.731019" + }, + { + "@id": "comment-id/AI4-001/5", + "@type": "Comment", + "dateCreated": "2024-07-18T15:08:59.608458", + "text": "Some compound may have been lost in the aqueous phase during the extraction", + "author": { + "@id": "./author/7" + } + }, + { + "@id": "./author/7", + "@type": "Person", + "givenName": "Joe", + "familyName": "Davies", + "email": "joseph.davies@nottingham.ac.uk" + } + ] +} +``` \ No newline at end of file diff --git a/examples/AI4Green/README_template.md b/examples/AI4Green/README_template.md new file mode 100644 index 0000000..dfd27f3 --- /dev/null +++ b/examples/AI4Green/README_template.md @@ -0,0 +1,26 @@ +# AI4Green + +## Information + +* Repo: https://github.com/AI4Green/AI4Green +* Website: https://ai4green.app/ + +### Structure of the AI4Green example + +Key parts of the reaction dataset are: +- The text field which renders the summary table in HTML +- Automatically generated .RDF (reaction data file) attachment and any additional file attachments + +## Concepts used + +Here is a correspondance between concepts in AI4Green and how they are translated in the metadata json file in the archive: + +| AI4Green concepts | JSON property | +|-------------------|------------------------| +| summary_table | text || +| comment | comment | +| mimetype | encodingFormat | +| time_of_creation | dateCreated || +| time_of_update | dateModified | +| author | author || +| name | name |