Finding a Findable Dataset#
About this interactive 
recipe
Author(s): Stuart Chalk
Topic(s): How and where to find a ‘findable’ chemical dataset
Format(s): Interactive Jupyter Notebook (Python)
Scenario(s): You are looking for research data to complement your compare with your own data
Skill(s): You should be familiar with
Learning outcomes: After completing this example you should understand:
How to make a request to a website using the Python ‘requests’ functionality
Retrieve data in JSON format and how to parse it (knowing the data model)
How to store confidential data in a remote file
How programmtically you can authenticate to an API (one of many ways)
Citation: ‘Finding a Findable Dataset’, Stuart Chalk, The IUPAC FAIR Chemistry Cookbook, Contributed: 2024-02-14 https://w3id.org/ifcc/IFCC013.
Reuse: This notebook is made available under a CC-BY-4.0 license.
Scenario#
Our group has a set of thermophysical data on over 8000 chemical substances. We want to integrate into this dataset another physical property dataset so that we can do an analysis of the correlations of the thermophysical data with the chosen physical property of the substances (that are common to both sets).
Criteria for picking the physical property dataset: high quality, trusted, large, available with an open license, so I can publish the results and make the derived dataset open.
High quality means: unambiguous identification of each chemical substance, enough contextual information (metadata) to make the values scientifically useful, i.e., at least the composition of the solvent, the temperature and for volatile substances the pressure.
Trusted means: the provenance chain is reported with the data, and it shows that the data comes from a reputable source(s) and any aggregation and/or processing is documented in enough detail that the community can understand how the dataset has been created/provided.
Step 1 - Searching PubChem for datasets#
Pubchem houses a lot of data about chemical substances, compounds and bioassays. Over time external organizations have worked with PubChem to include data, in one of a couple of ways:
data that has been integrated into PubChem pages (e.g., CCDC -> example)
data that is not available in a PubChem page but is available via the data sources section of the site as ‘annotations’ (e.g. RCSB PDB -> Example)
The data available is may not be structured and or clearly described, however if the source has a website with an API then you are likely to get better quality metadata from the linked site.
1.1 - Load the Python functions#
# as these are direct imports (they do not reference a Python package) they are built into Python
import requests
import json
1.2 - Search for sources that have ‘curation efforts’#
# This URL is the metadata about the data sources in PubChem
url = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/sourcetable/all/JSON/?response_type=display'
response = requests.get(url)
srcs = response.json()
results = []
search = 'Curation Efforts' # i.e., a repository, or other type of data source (this is in index 8 of the data list for each source)
rows = srcs['Table']['Row']
for row in rows:
if row['Cell'][8].find(search) != -1:
hit = {}
hit.update({'name': row['Cell'][0]})
hit.update({'url': row['Cell'][9]})
results.append(hit)
# when printed this is a scrollable list of many entries
print(json.dumps(results, indent=4))
[
{
"name": "Agency for Toxic Substances and Disease Registry (ATSDR)",
"url": "https://www.atsdr.cdc.gov/"
},
{
"name": "Alliance of Genome Resources",
"url": "https://www.alliancegenome.org/"
},
{
"name": "Analytical Resources Core (ARC), Colorado State University (CSU)",
"url": "https://www.research.colostate.edu/arc/"
},
{
"name": "Athena Minerals",
"url": "https://athena.unige.ch/athena/mineral/mineral.html"
},
{
"name": "Barrie Walker, BARK Information Services",
"url": "https://uk.linkedin.com/in/barrie-walker-85b4a510"
},
{
"name": "Beilstein Journals",
"url": "https://www.beilstein-institut.de/en/"
},
{
"name": "BindingDB",
"url": "https://www.bindingdb.org/rwd/bind/"
},
{
"name": "BioCyc",
"url": "https://biocyc.org/"
},
{
"name": "BioGRID",
"url": "https://thebiogrid.org/"
},
{
"name": "BRENDA: Enzyme Functional Data",
"url": "https://www.brenda-enzymes.org/"
},
{
"name": "CAMEO Chemicals",
"url": "https://cameochemicals.noaa.gov/"
},
{
"name": "Catalogue of Life (COL)",
"url": "https://www.catalogueoflife.org/"
},
{
"name": "CCSbase",
"url": "https://ccsbase.net/"
},
{
"name": "Cell Line Ontology (CLO)",
"url": ""
},
{
"name": "Cell Ontology (CL)",
"url": "https://obophenotype.github.io/cell-ontology/"
},
{
"name": "ChEBI",
"url": "https://www.ebi.ac.uk/chebi/"
},
{
"name": "ChEMBL",
"url": "https://www.ebi.ac.uk/chembl/"
},
{
"name": "Chemical Probes Portal",
"url": "https://www.chemicalprobes.org/"
},
{
"name": "ChemIDplus",
"url": "https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus"
},
{
"name": "Chemoproteomic Metabolic Pathway Resource, Scripps University",
"url": ""
},
{
"name": "Chris Southan",
"url": "https://www.ed.ac.uk/medicine-vet-medicine"
},
{
"name": "Commission on New Minerals, Nomenclature and Classification (CNMNC)",
"url": "http://cnmnc.units.it/"
},
{
"name": "Comparative Toxicogenomics Database (CTD)",
"url": "http://ctdbase.org/"
},
{
"name": "Cosmetic Ingredient Review (CIR)",
"url": "https://cir-safety.org/"
},
{
"name": "COVID-19 Disease Map",
"url": "https://covid.pages.uni.lu/"
},
{
"name": "Database of Interacting Proteins (DIP)",
"url": "https://dip.doe-mbi.ucla.edu/"
},
{
"name": "Drug Gene Interaction database (DGIdb)",
"url": "https://dgidb.org/"
},
{
"name": "Drug Induced Liver Injury Rank (DILIrank) Dataset",
"url": "https://www.fda.gov/science-research/liver-toxicity-knowledge-base-ltkb/drug-induced-liver-injury-rank-dilirank-dataset"
},
{
"name": "DrugBank",
"url": "https://www.drugbank.ca/"
},
{
"name": "DrugCentral",
"url": "http://drugcentral.org"
},
{
"name": "E. coli Metabolome Database (ECMDB)",
"url": "https://ecmdb.ca/"
},
{
"name": "Egon Willighagen, Department of Bioinformatics - BiGCaT, Maastricht University",
"url": "https://www.maastrichtuniversity.nl/el-willighagen"
},
{
"name": "Encyclopedia of Life (EOL)",
"url": "https://eol.org/"
},
{
"name": "EPA Air Toxics",
"url": "https://www3.epa.gov/ttn/atw/index.html"
},
{
"name": "EPA DSSTox",
"url": "https://www.epa.gov/chemical-research/distributed-structure-searchable-toxicity-dsstox-database"
},
{
"name": "FDA Global Substance Registration System (GSRS)",
"url": "https://www.fda.gov/industry/fda-data-standards-advisory-board/fdas-global-substance-registration-system"
},
{
"name": "FDA Orange Book",
"url": "https://www.fda.gov/drugs/drug-approvals-and-databases/approved-drug-products-therapeutic-equivalence-evaluations-orange-book"
},
{
"name": "FDA Pharm Classes",
"url": "https://www.fda.gov/industry/structured-product-labeling-resources/pharmacologic-class"
},
{
"name": "FlyBase",
"url": "https://flybase.org/"
},
{
"name": "Gene Curation Coalition (GenCC)",
"url": "https://thegencc.org/"
},
{
"name": "Gene Ontology (GO)",
"url": "http://geneontology.org/"
},
{
"name": "Genomics of Drug Sensitivity in Cancer (GDSC)",
"url": "https://www.cancerrxgene.org/"
},
{
"name": "Gloriam Group: Pharmaceutical informatics - Department of Drug Design and Pharmacology, University of Copenhagen",
"url": ""
},
{
"name": "Glycan Naming and Subsumption Ontology (GNOme)",
"url": "https://gnome.glyomics.org/"
},
{
"name": "GlycoNAVI",
"url": "https://glyconavi.org/"
},
{
"name": "GlyConnect",
"url": "https://glyconnect.expasy.org/"
},
{
"name": "GlyGen",
"url": "https://www.glygen.org/"
},
{
"name": "Handbook of Mineralogy",
"url": "https://handbookofmineralogy.org/"
},
{
"name": "Haz-Map, Information on Hazardous Chemicals and Occupational Diseases",
"url": "https://haz-map.com/"
},
{
"name": "Hazardous Chemical Information System (HCIS), Safe Work Australia",
"url": "http://hcis.safeworkaustralia.gov.au/"
},
{
"name": "Hazardous Substances Data Bank (HSDB)",
"url": "https://www.nlm.nih.gov/toxnet/index.html"
},
{
"name": "HUGO Gene Nomenclature Committee (HGNC)",
"url": "https://www.genenames.org/"
},
{
"name": "Human Metabolome Database (HMDB)",
"url": "https://hmdb.ca/"
},
{
"name": "Human Protein Atlas (HPA)",
"url": "https://www.proteinatlas.org/"
},
{
"name": "ILO-WHO International Chemical Safety Cards (ICSCs)",
"url": "https://chemicalsafety.ilo.org/dyn/icsc/showcard.home"
},
{
"name": "INOH",
"url": ""
},
{
"name": "IntAct Molecular Interaction Database",
"url": "https://www.ebi.ac.uk/intact/"
},
{
"name": "InterPro",
"url": "https://www.ebi.ac.uk/interpro/"
},
{
"name": "IUPAC Digitized pKa Dataset",
"url": "https://github.com/IUPAC/Dissociation-Constants"
},
{
"name": "IUPAC Periodic Table of the Elements and Isotopes (IPTEI)",
"url": "https://iupac.org/iptei/"
},
{
"name": "IUPHAR/BPS Guide to PHARMACOLOGY",
"url": "https://www.guidetopharmacology.org/"
},
{
"name": "KEGG",
"url": "https://www.genome.jp/kegg/kegg2.html"
},
{
"name": "KNApSAcK Species-Metabolite Database",
"url": "http://www.knapsackfamily.com/KNApSAcK/"
},
{
"name": "Kruve Lab, Ionization & Mass Spectrometry, Stockholm University",
"url": "https://kruvelab.com/"
},
{
"name": "Lab and Research Safety, University of Minnesota",
"url": ""
},
{
"name": "LIPID MAPS",
"url": "https://lipidmaps.org/"
},
{
"name": "LOTUS - the natural products occurrence database",
"url": "https://lotus.naturalproducts.net/"
},
{
"name": "MarkerDB",
"url": "https://markerdb.ca/"
},
{
"name": "Medical Subject Headings (MeSH)",
"url": "https://www.ncbi.nlm.nih.gov/mesh"
},
{
"name": "Molecular Imaging and Contrast Agent Database (MICAD)",
"url": "https://www.ncbi.nlm.nih.gov/books/NBK5330/"
},
{
"name": "Molecular Imaging Database (MOLI)",
"url": ""
},
{
"name": "Mouse Genome Informatics (MGI)",
"url": "https://www.informatics.jax.org/"
},
{
"name": "Natural Product Activity and Species Source (NPASS)",
"url": "https://bidd.group/NPASS/"
},
{
"name": "NCI Thesaurus (NCIt)",
"url": "https://ncit.nci.nih.gov/ncitbrowser/"
},
{
"name": "NEQUIM - Chemoinformatics Group",
"url": "http://nequim.qui.ufmg.br/"
},
{
"name": "NextMove Software",
"url": "https://www.nextmovesoftware.com/"
},
{
"name": "NIAID ChemDB",
"url": "https://chemdb.niaid.nih.gov/"
},
{
"name": "NIST Chemistry WebBook",
"url": ""
},
{
"name": "NITE-CMC",
"url": "https://www.nite.go.jp/en/chem/"
},
{
"name": "Online Mendelian Inheritance in Man (OMIM)",
"url": "https://omim.org/"
},
{
"name": "Open Targets",
"url": "https://www.opentargets.org/"
},
{
"name": "PANTHER",
"url": "http://www.pantherdb.org/"
},
{
"name": "PathBank",
"url": "https://pathbank.org/"
},
{
"name": "Pathway Interaction Database",
"url": ""
},
{
"name": "Pfam",
"url": "https://www.ebi.ac.uk/interpro/"
},
{
"name": "PharmGKB",
"url": "https://www.pharmgkb.org/"
},
{
"name": "Pharos",
"url": "https://pharos.nih.gov/"
},
{
"name": "Pistoia Alliance DataFAIRy Bioassay Pilot",
"url": "https://www.pistoiaalliance.org/projects/current-projects/datafairy-project/"
},
{
"name": "Plant Reactome",
"url": "https://plantreactome.gramene.org/index.php?lang=en"
},
{
"name": "PlantCyc",
"url": "https://www.plantcyc.org/"
},
{
"name": "PomBase: Fission Yeast Resource",
"url": "https://www.pombase.org/"
},
{
"name": "Protein Ontology",
"url": "https://proconsortium.org/"
},
{
"name": "Rat Genome Database (RGD)",
"url": "https://rgd.mcw.edu/"
},
{
"name": "RCSB Protein Data Bank (RCSB PDB)",
"url": "https://www.rcsb.org/"
},
{
"name": "Reactome",
"url": "https://reactome.org/"
},
{
"name": "Rhea - Annotated Reactions Database",
"url": "https://www.rhea-db.org/"
},
{
"name": "Risk Assessment Information System (RAIS)",
"url": "https://rais.ornl.gov/"
},
{
"name": "RRUFF Project",
"url": "https://rruff.info/"
},
{
"name": "Saccharomyces Genome Database (SGD)",
"url": "https://www.yeastgenome.org/"
},
{
"name": "STRING: functional protein association networks",
"url": "https://string-db.org/"
},
{
"name": "SureChEMBL",
"url": "https://www.surechembl.org/"
},
{
"name": "Swiss Institute of Bioinformatics Bgee",
"url": "https://www.bgee.org/"
},
{
"name": "Swiss Institute of Bioinformatics Cellosaurus",
"url": "https://www.cellosaurus.org/"
},
{
"name": "Swiss Institute of Bioinformatics ENZYME",
"url": "https://enzyme.expasy.org/"
},
{
"name": "Swiss Institute of Bioinformatics neXtProt",
"url": "https://www.nextprot.org/"
},
{
"name": "Symbol Nomenclature for Glycans (SNFG) Reference Collection",
"url": "https://www.ncbi.nlm.nih.gov/glycans/snfg.html"
},
{
"name": "The Cambridge Structural Database",
"url": ""
},
{
"name": "The National Institute for Occupational Safety and Health (NIOSH)",
"url": "https://www.cdc.gov/niosh/npg/"
},
{
"name": "The Natural Products Atlas",
"url": "https://www.npatlas.org/"
},
{
"name": "The University of Alabama Libraries",
"url": "https://ir.ua.edu/"
},
{
"name": "The Zebrafish Information Network (ZFIN)",
"url": "https://zfin.org/"
},
{
"name": "Therapeutic Target Database (TTD)",
"url": "https://db.idrblab.net/ttd/"
},
{
"name": "Toxin and Toxin Target Database (T3DB)",
"url": "http://www.t3db.ca/"
},
{
"name": "UniCarbKB",
"url": ""
},
{
"name": "UniProt",
"url": "https://www.uniprot.org/"
},
{
"name": "UVCBs and Multi-Constituent Substances (MCS) Committee",
"url": "https://hesiglobal.org/uvcb/"
},
{
"name": "VEuPathDB: The Eukaryotic Pathogen, Vector and Host Informatics Resource",
"url": "https://veupathdb.org/"
},
{
"name": "Wikidata",
"url": "https://www.wikidata.org/wiki/Wikidata:Main_Page"
},
{
"name": "Wikipedia",
"url": "https://en.wikipedia.org/wiki/Main_Page"
},
{
"name": "World Register of Marine Species (WoRMS)",
"url": "https://www.marinespecies.org/"
},
{
"name": "WormBase",
"url": "https://wormbase.org/"
},
{
"name": "Xenbase",
"url": "https://www.xenbase.org/"
},
{
"name": "Yeast Metabolome Database (YMDB)",
"url": "http://www.ymdb.ca/"
}
]
Step 2 - Searching FAIR Sharing for datasets#
FAIRSharing is a database of FAIR resources and per se a database of datasets, however you might find a repository here that has the kind of data you are looking for. The code below accesses the FAIR sharing API so search for ‘chemistry’ (or other term) related resources.
Note: To use the code below please go to https://fairsharing.org/accounts/signup, create an account and then enter your username and password in the quotes for ‘fs_user’ and ‘fs_pass’ below.
2.1 - Authentication to the FAIRSharing API#
# see https://fairsharing.org/API_doc for instructions on how to search the API
# user login
fs_user = "ChemCookbook"
fs_pass = "ydt_wdh_MRD*qut5xvq"
url = 'https://api.fairsharing.org/users/sign_in'
loghdrs = {'Accept': 'application/json','Content-Type': 'application/json'}
login = {'user': {'login': fs_user, 'password': fs_pass}}
response = requests.request("POST", url, headers=loghdrs, data=json.dumps(login))
data = response.json()
print(data)
{'success': True, 'jwt': 'eyJhbGciOiJIUzI1NiJ9.eyJqdGkiOiI0YjVkNzQyMi1hOTg3LTRlZWYtYjQyYi1hN2U3Yjc2MTM0ZTEiLCJzdWIiOiI4NTA5Iiwic2NwIjoidXNlciIsImF1ZCI6bnVsbCwiaWF0IjoxNzQ1OTM1MTQ3LCJleHAiOjE3NDYwMjE1NDd9.1_jnoh-pZu3g4RlYQlwLSJPSjoptGSexA4FYxr2lwaQ', 'username': 'ChemCookbook', 'id': 8509, 'role': 'user', 'profile_type': 'none', 'watched_records': [], 'is_curator': False, 'is_super_curator': False, 'third_party': False, 'expiry': 1746021547, 'message': 'Authentication successful'}
2.2 - Make the API request#
# in order to authenticate when making an API request the 'jwt' code above must
# be included in the JSON headers (see https://en.wikipedia.org/wiki/List_of_HTTP_header_fields)
jwt = data['jwt']
srchdrs = {'Accept': 'application/json', 'Content-Type': 'application/json', 'Authorization': "Bearer {0}".format(jwt)}
searchterm = 'chemistry'
searchurl ='https://api.fairsharing.org/search/fairsharing_records?q=' + searchterm
search = requests.request("POST", searchurl, headers=srchdrs)
hits = json.loads(search.content)
# this prints out the raw JSON for the first entry (the 'data' entry is a JSON list)
# that is returned from the API request (formatted nicely, which means its on many lines)
print(json.dumps(hits['data'][0], indent=4))
{
"id": "2948",
"type": "fairsharing_records",
"attributes": {
"created_at": "2020-04-15T07:17:37.000Z",
"updated_at": "2025-01-16T13:19:01.582Z",
"metadata": {
"doi": "10.25504/FAIRsharing.KOiDmy",
"name": "EMODnet Chemistry",
"status": "ready",
"contacts": [
{
"contact_name": "EMODnet",
"contact_email": "secretariat@emodnet.eu"
}
],
"homepage": "https://emodnet.ec.europa.eu/en/chemistry",
"citations": [],
"identifier": 2948,
"description": "The EMODnet Chemistry portal provides easy access to marine chemical data, standardised harmonized validated data collections and reliable data products, highly relevant to assess ecosystem status according to the Marine Strategy Framework Directive. Data on temporal and spatial distribution of marine litter, of the concentration of nutrients, organic matter, pesticides, heavy metals, radionuclides and antifoulants in the water column, in the sediment and in biota.",
"abbreviation": "EMODnet Chemistry",
"data_curation": {
"type": "not found"
},
"support_links": [
{
"url": "https://www.emodnet-chemistry.eu/help/contact?10",
"name": "Contact us",
"type": "Contact form"
},
{
"url": "https://www.emodnet-chemistry.eu/help",
"name": "FAQ",
"type": "Help documentation"
},
{
"url": "https://www.emodnet-chemistry.eu/about",
"name": "About",
"type": "Help documentation"
},
{
"url": "https://www.emodnet-chemistry.eu/data",
"name": "About the Data",
"type": "Help documentation"
},
{
"url": "https://www.emodnet-chemistry.eu/products",
"name": "About Data Products",
"type": "Help documentation"
},
{
"url": "https://www.emodnet-chemistry.eu/documents",
"name": "Documents",
"type": "Help documentation"
},
{
"url": "https://www.emodnet-chemistry.eu/newsevents",
"name": "News",
"type": "Help documentation"
}
],
"year_creation": 2009,
"data_versioning": "yes",
"associated_tools": [
{
"url": "https://www.emodnet-chemistry.eu/tools",
"name": "Data Management Tools"
}
],
"data_access_condition": {
"type": "open"
},
"data_contact_information": "yes",
"data_deposition_condition": {
"url": "https://emodnet.ec.europa.eu/en/contribute-data-emodnet",
"type": "open"
},
"citation_to_related_publications": "no",
"data_access_for_pre_publication_review": "no"
},
"legacy_ids": [
"biodbcore-001452",
"bsg-d001452"
],
"name": "FAIRsharing record for: EMODnet Chemistry",
"abbreviation": "EMODnet Chemistry",
"url": "https://fairsharing.org/10.25504/FAIRsharing.KOiDmy",
"doi": "10.25504/FAIRsharing.KOiDmy",
"fairsharing_licence": "https://creativecommons.org/licenses/by-sa/4.0/. Please link to https://fairsharing.org and https://api.fairsharing.org/img/fairsharing-attribution.svg for attribution.",
"description": "This FAIRsharing record describes: The EMODnet Chemistry portal provides easy access to marine chemical data, standardised harmonized validated data collections and reliable data products, highly relevant to assess ecosystem status according to the Marine Strategy Framework Directive. Data on temporal and spatial distribution of marine litter, of the concentration of nutrients, organic matter, pesticides, heavy metals, radionuclides and antifoulants in the water column, in the sediment and in biota.",
"linked_records": [],
"linking_records": [],
"fairsharing_registry": "Database",
"record_type": "repository",
"subjects": [
"Environmental Science",
"Geography",
"Earth Science",
"Oceanography"
],
"domains": [
"Geographical location",
"Marine environment"
],
"taxonomies": [
"Not applicable"
],
"user_defined_tags": [
"Geographic Information System (GIS)",
"Marine Chemistry"
],
"countries": [
"European Union"
],
"publications": [
{
"id": 501,
"pubmed_id": null,
"title": "JRC Technical report: marine litter database",
"year": 2019,
"url": "http://doi.org/10.2760/621710",
"authors": "EU publications",
"journal": "Luxembourg: Publications Office of the European Union, 2018",
"doi": "10.2760/621710",
"created_at": "2021-09-30T08:23:14.415Z",
"updated_at": "2021-09-30T11:28:29.493Z"
},
{
"id": 2862,
"pubmed_id": null,
"title": "JRC Technical Reports: EU marine beach litter baselines",
"year": 2020,
"url": "http://doi.org/10.2760/16903",
"authors": "del Mar Chaves Montero, Maria\u00a0;\u00a0\u00a0Brosich, Alberto\u00a0;\u00a0\u00a0Hanke, Georg\u00a0;\u00a0\u00a0Loon, Willem van\u00a0;\u00a0\u00a0Addamo, Anna Maria\u00a0;\u00a0\u00a0Walvoort, Dennis\u00a0;\u00a0\u00a0Vinci, Matteo\u00a0;\u00a0\u00a0Molina Jack, Maria Eugenia\u00a0;\u00a0\u00a0Giorgetti, Alessandra",
"journal": "Publications Office of the European Union, Luxemburg",
"doi": "10.2760/16903",
"created_at": "2021-09-30T08:27:52.129Z",
"updated_at": "2021-09-30T11:28:37.877Z"
},
{
"id": 2863,
"pubmed_id": null,
"title": "EMODnet marine litter data management at pan-European scale",
"year": 2019,
"url": "http://doi.org/doi.org/10.1016/j.ocecoaman.2019.104930",
"authors": "Maria Eugenia Molina Jack, Maria del Mar Chaves Montero, Fran\u00e7ois Galgani, Alessandra Giorgetti, Matteo Vinci, Morgan Le Moigne, Alberto Brosich",
"journal": "Ocean & Coastal Management",
"doi": "doi.org/10.1016/j.ocecoaman.2019.104930",
"created_at": "2021-09-30T08:27:52.244Z",
"updated_at": "2021-09-30T11:28:37.976Z"
},
{
"id": 2864,
"pubmed_id": null,
"title": "Toward the Integrated Marine Debris Observing System",
"year": 2019,
"url": "http://doi.org/10.3389/fmars.2019.00447",
"authors": "Maximenko Nikolai, Corradi Paolo, Law Kara Lavender, Van Sebille Erik, Garaba Shungudzemwoyo P., Lampitt Richard Stephen, Galgani Francois, Martinez-Vicente Victor, Goddijn-Murphy Lonneke, Veiga Joana Mira, Thompson Richard C., Maes Christophe, Moller Delwyn, L\u00f6scher Carolin Regina, Addamo Anna Maria, Lamson Megan R., Centurioni Luca R., Posth Nicole R., Lumpkin Rick, Vinci Matteo, Martins Ana Maria, Pieper Catharina Diogo, Isobe Atsuhiko, Hanke Georg, Edwards Margo, Chubarenko Irina P., Rodriguez Ernesto, Aliani Stefano, Arias Manuel, Asner Gregory P., Brosich Alberto, Carlton James T., Chao Yi, Cook Anna-Marie, Cundy Andrew B., Galloway Tamara S., Giorgetti Alessandra, Goni Gustavo Jorge, Guichoux Yann, Haram Linsey E., Hardesty Britta Denise, Holdsworth Neil, Lebreton Laurent, Leslie Heather A., Macadam-Somer Ilan, Mace Thomas, Manuel Mark, Marsh Robert, Martinez Elodie, Mayor Daniel J., Le Moigne Morgan, Molina Jack Maria Eugenia, Mowlem Matt Charles, Obbard Rachel W., Pabortsava Katsiaryna, Robberson Bill, Rotaru Amelia-Elena, Ruiz Gregory M., Spedicato Maria Teresa, Thiel Martin, Turra Alexander, Wilcox Chris",
"journal": "Frontiers in Marine Science",
"doi": "10.3389/fmars.2019.00447",
"created_at": "2021-09-30T08:27:52.419Z",
"updated_at": "2021-09-30T11:28:38.068Z"
},
{
"id": 2865,
"pubmed_id": null,
"title": "The European Marine Observation and Data Network (EMODnet): Visions and Roles of the Gateway to Marine Data in Europe",
"year": 2019,
"url": "http://doi.org/10.3389/fmars.2019.00313",
"authors": "Bel\u00e9n Mart\u00edn M\u00edguez, Antonio Novellino, Matteo Vinci,\u00a0Simon Claus,\u00a0Jan-Bart Calewaert,\u00a0Henry Vallius,\u00a0Thierry Schmitt,\u00a0Alessandro Pititto,\u00a0Alessandra Giorgetti,\u00a0Natalie Askew,\u00a0Sissy Iona,\u00a0Dick Schaap,\u00a0Nadia Pinardi,\u00a0Quillon Harpham,\u00a0Belinda J. Kater,\u00a0Jacques Populus,\u00a0Jun She,\u00a0Atanas Vasilev Palazov,\u00a0Oonagh McMeel,\u00a0Paula Oset,\u00a0Dan Lear,\u00a0Giuseppe M. R. Manzella,\u00a0Patrick Gorringe,\u00a0Simona Simoncelli,\u00a0Kate Larkin,\u00a0Neil Holdsworth,\u00a0Christos Dimitrios Arvanitidis,\u00a0Maria Eugenia Molina Jack,\u00a0Maria del Mar Chaves Montero,\u00a0 Peter M. J. Herman, Francisco Hernandez",
"journal": "Frontiers in Marine Science",
"doi": "10.3389/fmars.2019.00313",
"created_at": "2021-09-30T08:27:52.536Z",
"updated_at": "2021-09-30T11:28:38.234Z"
},
{
"id": 2869,
"pubmed_id": null,
"title": "Maritime spatial planning supported by infrastructure for spatial information in Europe (INSPIRE)",
"year": 2018,
"url": "http://doi.org/10.1016/j.ocecoaman.2017.11.007",
"authors": "Andrej Abramic, Emanuele Bigagli, Vittorio Barale, Michael Assouline, Alberto Lorenzo-Alonsoce, Conor Norton",
"journal": "Ocean & Coastal Management",
"doi": "10.1016/j.ocecoaman.2017.11.007",
"created_at": "2021-09-30T08:27:53.175Z",
"updated_at": "2021-09-30T11:28:38.334Z"
},
{
"id": 2870,
"pubmed_id": null,
"title": "EMODnet CHEMISTRY \u2013 DATA AGGREGATION AND PRODUCT GENERATIONS IN THE BLACK SEA",
"year": 2018,
"url": "https://www.emodnet-chemistry.eu/repository/Paper_Jepe_Bugaetal_2018.pdf",
"authors": "L. Buga, L. Boicenco, A. Giorgetti, G. Sarbu, A. Spinu",
"journal": "Journal of Environmental Protection and Ecology",
"doi": null,
"created_at": "2021-09-30T08:27:53.277Z",
"updated_at": "2021-09-30T11:28:38.434Z"
},
{
"id": 2871,
"pubmed_id": null,
"title": "The role of EMODnet Chemistry in the European challenge for Good Environmental Status",
"year": 2016,
"url": "http://doi.org/10.5194/nhess-17-197-2017",
"authors": "Matteo Vinci,\u00a0Alessandra Giorgetti,\u00a0and Marina Lipizer",
"journal": "Nat. Hazards Earth Syst. Sci., 17, 197\u2013204, 2017",
"doi": "10.5194/nhess-17-197-2017",
"created_at": "2021-09-30T08:27:53.420Z",
"updated_at": "2021-09-30T11:28:38.526Z"
},
{
"id": 2900,
"pubmed_id": null,
"title": "EMODnet Chemistry Spatial Data Infrastructure for marine observations and related information",
"year": 2018,
"url": "http://doi.org/doi.org/10.1016/j.ocecoaman.2018.03.016",
"authors": "A.GiorgettiaE.PartescanoaA.BarthbL.BugacJ.GattidG.GiorgieA.IonafM.LipizeraN.HoldsworthgM.M.LarsenhD.SchaapiM.VinciaM.Wenzerj",
"journal": "Ocean & Coastal Management",
"doi": "doi.org/10.1016/j.ocecoaman.2018.03.016",
"created_at": "2021-09-30T08:27:57.138Z",
"updated_at": "2021-09-30T11:28:39.044Z"
}
],
"licence_links": [
{
"licence_name": "SeaDataNet Data Policy",
"licence_id": 742,
"licence_url": "https://www.emodnet-bathymetry.eu/metadata-amp-data/user-registration",
"link_id": 1386,
"relation": "undefined"
}
],
"grants": [
{
"id": 3816,
"fairsharing_record_id": 2948,
"organisation_id": 960,
"relation": "funds",
"created_at": "2021-09-30T09:26:27.420Z",
"updated_at": "2021-09-30T09:26:27.420Z",
"grant_id": null,
"is_lead": false,
"saved_state": {
"id": 960,
"name": "European Union (EU)",
"types": [
"Government body"
],
"is_lead": false,
"relation": "funds"
}
},
{
"id": 3815,
"fairsharing_record_id": 2948,
"organisation_id": 2234,
"relation": "maintains",
"created_at": "2021-09-30T09:26:27.397Z",
"updated_at": "2021-09-30T09:26:27.397Z",
"grant_id": null,
"is_lead": true,
"saved_state": {
"id": 2234,
"name": "OGS (Istituto Nazionale di Oceanografia e Geofisica Sperimentale)",
"types": [
"Research institute"
],
"is_lead": true,
"relation": "maintains"
}
},
{
"id": 3817,
"fairsharing_record_id": 2948,
"organisation_id": 937,
"relation": "maintains",
"created_at": "2021-09-30T09:26:27.446Z",
"updated_at": "2021-09-30T09:26:27.446Z",
"grant_id": null,
"is_lead": false,
"saved_state": {
"id": 937,
"name": "European Marine Observation and Data Network (EMODnet)",
"types": [
"Consortium"
],
"is_lead": false,
"relation": "maintains"
}
}
],
"url_for_logo": null,
"exhaustive_licences": false
}
}
2.3 - Output the data in a presentable format#
# here we loop over the data that has been returned and print it out, one per line
for hit in hits['data']:
print(hit['attributes']['name'] + ": " + hit['attributes']['url'])
FAIRsharing record for: EMODnet Chemistry: https://fairsharing.org/10.25504/FAIRsharing.KOiDmy
FAIRsharing record for: Portable reduced-precision binary format for trajectories produced by GROMACS package.: https://fairsharing.org/10.25504/FAIRsharing.cb1adb
FAIRsharing record for: Chemistry: https://fairsharing.org/fairsharing_records/3524
FAIRsharing record for: Royal Society of Chemistry - Data policy: https://fairsharing.org/10.25504/FAIRsharing.egbgwm
FAIRsharing record for: BindingDB database of measured binding affinities: https://fairsharing.org/10.25504/FAIRsharing.3b36hk
FAIRsharing record for: Chemistry vocabulary: https://fairsharing.org/10.25504/FAIRsharing.TrcBD2
FAIRsharing record for: MINAS - A Database of Metal Ions in Nucleic AcidS: https://fairsharing.org/10.25504/FAIRsharing.wqtfkv
FAIRsharing record for: Beilstein Journal of Organic Chemistry: https://fairsharing.org/10.25504/FAIRsharing.7GA79k
FAIRsharing record for: EPA CompTox Chemicals Dashboard: https://fairsharing.org/10.25504/FAIRsharing.tfj7gt
FAIRsharing record for: ChemSpider: https://fairsharing.org/10.25504/FAIRsharing.96f3gm
FAIRsharing record for: ioChem-BD: https://fairsharing.org/10.25504/FAIRsharing.lwW6a1
FAIRsharing record for: CAS Registry Number: https://fairsharing.org/10.25504/FAIRsharing.r7Kwy7
FAIRsharing record for: Chemical Markup Language: https://fairsharing.org/10.25504/FAIRsharing.3mdt9n
FAIRsharing record for: Elsevier / American Society for Biochemistry and Molecular Biology - Journal of Biological Chemistry - Data Policy: https://fairsharing.org/fairsharing_records/5290
FAIRsharing record for: NFDI4Chem : https://fairsharing.org/fairsharing_records/5027
FAIRsharing record for: Chemical Abstracts Service Common Chemistry: https://fairsharing.org/10.25504/FAIRsharing.e5c86e
FAIRsharing record for: IUPAC International Chemical Identifier: https://fairsharing.org/10.25504/FAIRsharing.ddk9t9
FAIRsharing record for: CHARMM Card File Format: https://fairsharing.org/10.25504/FAIRsharing.7hp91k
FAIRsharing record for: Allotrope Data Format: https://fairsharing.org/10.25504/FAIRsharing.26e0d8
FAIRsharing record for: Swedish Ocean Archive: https://fairsharing.org/10.25504/FAIRsharing.npf403
FAIRsharing record for: Reaction InChI: https://fairsharing.org/10.25504/FAIRsharing.58b6f9
FAIRsharing record for: VDJdb: a curated database of T-cell receptors with known antigen specificity: https://fairsharing.org/10.25504/FAIRsharing.nwz68
FAIRsharing record for: Dot Bracket Notation (DBN) - Vienna Format: https://fairsharing.org/10.25504/FAIRsharing.4xrzw1
FAIRsharing record for: Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics: https://fairsharing.org/10.25504/FAIRsharing.207caf
FAIRsharing record for: Chemical Methods Ontology: https://fairsharing.org/10.25504/FAIRsharing.9j4wh2