Thymidine
Everything that changed this flow. Back to the flow
4694bc86-12ab-47d7-adf4-95b8b60e7174
By field
13 fields| Field | Changes | Written by | Latest note |
|---|---|---|---|
| properties | 6 | enrich_references, link_flows_to_their_substance, normalise_property_values, opsin_iupac, rdkit_post_consensus, rdkit_pre_consensus | the substance's answer, copied onto its flow |
| altLabel | 3 | chebi_altlabels, consensus_match, strip_catalogue_altlabels | Removed 1 catalogue altLabel value(s): 'NSC 21548' (registry code) |
| prefLabel | 2 | bootstrap_labels, normalize_name_case | Title-cased words without internal capitals (preserved words with uppercase letters beyond the first character) |
| cas_match_labels | 1 | consensus_match | group_key=thymidine||dimension=Environmental > media=Ground > geography=Agricultural; group_sources=['chebi', 'ec_inventory', 'pubchem']; cas_sources={'50-89-5': ['chebi', 'ec_inventory', 'pubchem']}; assigned CAS labels from group consensus; object_uuid=fo-561a72e2ad99f518: {'50-89-5': 'exactMatch'} |
| concept_associations | 1 | carry_associations_onto_flows | associations resolved on the elementary layer |
| context | 1 | default_context_mapping | Mapped from context mapping for source=EF 3.1, source context Emissions > Emissions to water > Emissions to water, unspecified (long-term) |
| context_iri | 1 | default_context_mapping | Mapped from context mapping for source=EF 3.1, source context Emissions > Emissions to water > Emissions to water, unspecified (long-term) |
| name | 1 | bootstrap_labels | Purged legacy name field to enforce prefLabel usage |
| references | 1 | enrich_references | Added references with provenance; cas_numbers=['50-89-5']; matched_chebi_ids=['http://purl.obolibrary.org/obo/CHEBI_17748']; candidate_pubchem_cids=[1134, 5789, 72247, 159269, 165328, 253891, 445408, 451756, 3000346, 3995254, 5270603, 126963445, 156592083]; selected_pubchem_cids=[5789]; formula_similarity_expected=[]; pubchem_selection_rule=curated_cas_then_formula_similarity_then_prefer_chebi_aligned_when_unambiguous_else_keep_all_cas_matches; single_cas_commonchem_link=yes |
| skos_definition | 1 | enrich_references | Merged ChEBI/PubChem definitions into skos:definition |
| synonyms | 1 | bootstrap_labels | Removed legacy synonyms field in favor of structured labels |
| types | 1 | link_flows_to_their_substance | the substance's answer, copied onto its flow |
| unit_iri | 1 | unit_normalization | Unit IRI set from normalization of 'kg' |
Where several steps wrote one field, the last one won — and the log below shows the sequence.
Changes
21| # | Step | Field | From | To | Why |
|---|---|---|---|---|---|
| 14,339 | bootstrap_labels | prefLabel | — | [{"@value":"thymidine","@language":"en","source":{"prov:wasGeneratedBy":"bootstrap_labels","prov:wasAttributedTo":"cons… | Bootstrapped prefLabel from legacy name field |
| 14,340 | bootstrap_labels | name | thymidine | — | Purged legacy name field to enforce prefLabel usage |
| 14,341 | bootstrap_labels | synonyms | ["organic","thymidine"] | [] | Removed legacy synonyms field in favor of structured labels |
| 83,276 | default_context_mapping | context | — | {"dimension":"Environmental","media":"Water","water_body":"Long-term"} | Mapped from context mapping for source=EF 3.1, source context Emissions > Emissions to water > Emissions to water, unspecified (long-term) |
| 83,277 | default_context_mapping | context_iri | — | https://vocab.brightway.one/flow-contexts/envi-wate-lote | Mapped from context mapping for source=EF 3.1, source context Emissions > Emissions to water > Emissions to water, unspecified (long-term) |
| 218,074 | unit_normalization | unit_iri | — | https://vocab.brightway.one/units/unit/KiloGM | Unit IRI set from normalization of 'kg' |
| 224,410 | normalize_name_case | prefLabel | [{"@value":"thymidine","@language":"en","source":{"prov:wasGeneratedBy":"bootstrap_labels","prov:wasAttributedTo":"cons… | [{"@value":"Thymidine","@language":"en","source":{"prov:wasGeneratedBy":"bootstrap_labels","prov:wasAttributedTo":"cons… | Title-cased words without internal capitals (preserved words with uppercase letters beyond the first character) |
| 240,758 | enrich_references | properties | {} | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | Added ChEBI/PubChem properties (chebi_ids=1, pubchem_cids=1) |
| 240,759 | enrich_references | skos_definition | — | [{"@value":"A pyrimidine 2'-deoxyribonucleoside having thymine as the nucleobase.","@language":"en","provenance":{"prov… | Merged ChEBI/PubChem definitions into skos:definition |
| 240,760 | enrich_references | references | [] | [{"@id":"gmelin:282610","provenance":{"prov:wasGeneratedBy":"enrich_references.chebi_xrefs","prov:wasAttributedTo":"con… | Added references with provenance; cas_numbers=['50-89-5']; matched_chebi_ids=['http://purl.obolibrary.org/obo/CHEBI_17748']; candidate_pubchem_cids=[1134, 5789, 72247, 159269, 165328, 253891, 445408, 451756, 3000346, 3995254, 5270603, 126963445, 156592083]; selected_pubchem_cids=[5789]; formula_similarity_expected=[]; pubchem_selection_rule=curated_cas_then_formula_similarity_then_prefer_chebi_aligned_when_unambiguous_else_keep_all_cas_matches; single_cas_commonchem_link=yes |
| 252,224 | rdkit_pre_consensus | properties | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | rdkit_pre_consensus from 'CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O'; added: inchi2d_string, monoisotopic_mass |
| 256,305 | chebi_altlabels | altLabel | [] | [{"@value":"1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione","@language":"en","source":{"… | Added 9 ChEBI synonym(s) as altLabel from 1 linked ChEBI record(s) |
| 272,620 | consensus_match | altLabel | [{"@value":"1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione","@language":"en","source":{"… | [{"@value":"1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione","@language":"en","source":{"… | group_key=thymidine||dimension=Environmental > media=Ground > geography=Agricultural; cas=50-89-5; added Common Chemistry CAS names as altLabel: 1-(2-Deoxy-β-<span class="text-smallcaps">D</span>-<em>erythro</em>-pentofuranosyl)-5-methyl-2,4(1<em>H</em>,3<em>H</em>)-pyrimidinedione, 10: PN: CN101531718 PAGE: 4 claimed sequence, 2,4(1<em>H</em>,3<em>H</em>)-Pyrimidinedione, 1-(2-deoxy-β-<span class="text-smallcaps">D</span>-<em>erythro</em>-pentofuranosyl)-5-methyl-, 20: PN: WO2022263569 PAGE: 208 claimed sequence, 2′-Deoxythymidine, 31: PN: CN108866051 SEQID: 31 claimed sequence, 5-Methyl-2′-deoxyuridine, 5-Methyldeoxyuridine, 5: PN: CN104513856 PAGE: 2 claimed sequence, DThyd, Deoxyribothymidine, Doxribtimine, MeSH ID: D013936, NSC 21548, Thymidin, Thymine 2-desoxyriboside, Thymine deoxyriboside, Uridine, 2′-deoxy-5-methyl-, dT, β-<span class="text-smallcaps">D</span>-Ribofuranoside, thymine-1 2-deoxy-, β-Thymidine; object_uuid=fo-561a72e2ad99f518 |
| 272,621 | consensus_match | cas_match_labels | — | {"50-89-5":"exactMatch"} | group_key=thymidine||dimension=Environmental > media=Ground > geography=Agricultural; group_sources=['chebi', 'ec_inventory', 'pubchem']; cas_sources={'50-89-5': ['chebi', 'ec_inventory', 'pubchem']}; assigned CAS labels from group consensus; object_uuid=fo-561a72e2ad99f518: {'50-89-5': 'exactMatch'} |
| 277,419 | opsin_iupac | properties | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | opsin_iupac: set authoritative IUPAC name, SMILES, InChI from 'Thymidine' |
| 284,103 | rdkit_post_consensus | properties | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | rdkit_post_consensus from 'Cc1cn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O'; confirmed: smiles_string, inchi2d_string, inchi2d_key_string, molecular_formula, molecular_mass, monoisotopic_mass |
| 290,192 | strip_catalogue_altlabels | altLabel | [{"@value":"1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione","@language":"en","source":{"… | [{"@value":"1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione","@language":"en","source":{"… | Removed 1 catalogue altLabel value(s): 'NSC 21548' (registry code) |
| 322,652 | carry_associations_onto_flows | concept_associations | [] | [{"@type":"xkos:ConceptAssociation","xkos:sourceConcept":{"@id":"https://vocab.brightway.one/ef/3.1/flow/4694bc86-12ab-… | associations resolved on the elementary layer |
| 391,774 | normalise_property_values | properties | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | typed the way the ontology types it |
| 399,958 | link_flows_to_their_substance | types | — | ["https://w3id.org/chemrof/NeutralMolecule"] | the substance's answer, copied onto its flow |
| 399,959 | link_flows_to_their_substance | properties | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | {"https://w3id.org/chemrof/molecular_formula":{"@id":"https://w3id.org/chemrof/molecular_formula","@value":["C10H14N2O5… | the substance's answer, copied onto its flow |
PROV-O trail
21 activitiesOne activity per change: which version of the flow it consumed, and which it produced. The values are on the change with the same number — stored once, not twice.
| Activity | Field | Agent | Used | Generated |
|---|---|---|---|---|
| ef:activity/change/20260821T1302361922970000/14339 | prefLabel | ef:agent/bootstrap_labels | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v0 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v1 |
| ef:activity/change/20260821T1302361922970000/14340 | name | ef:agent/bootstrap_labels | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v1 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v2 |
| ef:activity/change/20260821T1302361922970000/14341 | synonyms | ef:agent/bootstrap_labels | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v2 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v3 |
| ef:activity/change/20260821T1302361922970000/83276 | context | ef:agent/default_context_mapping | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v3 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v4 |
| ef:activity/change/20260821T1302361922970000/83277 | context_iri | ef:agent/default_context_mapping | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v4 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v5 |
| ef:activity/change/20260821T1302361922970000/218074 | unit_iri | ef:agent/unit_normalization | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v5 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v6 |
| ef:activity/change/20260821T1302361922970000/224410 | prefLabel | ef:agent/normalize_name_case | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v6 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v7 |
| ef:activity/change/20260821T1302361922970000/240758 | properties | ef:agent/enrich_references | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v7 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v8 |
| ef:activity/change/20260821T1302361922970000/240759 | skos_definition | ef:agent/enrich_references | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v8 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v9 |
| ef:activity/change/20260821T1302361922970000/240760 | references | ef:agent/enrich_references | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v9 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v10 |
| ef:activity/change/20260821T1302361922970000/252224 | properties | ef:agent/rdkit_pre_consensus | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v10 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v11 |
| ef:activity/change/20260821T1302361922970000/256305 | altLabel | ef:agent/chebi_altlabels | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v11 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v12 |
| ef:activity/change/20260821T1302361922970000/272620 | altLabel | ef:agent/consensus_match | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v12 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v13 |
| ef:activity/change/20260821T1302361922970000/272621 | cas_match_labels | ef:agent/consensus_match | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v13 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v14 |
| ef:activity/change/20260821T1302361922970000/277419 | properties | ef:agent/opsin_iupac | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v14 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v15 |
| ef:activity/change/20260821T1302361922970000/284103 | properties | ef:agent/rdkit_post_consensus | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v15 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v16 |
| ef:activity/change/20260821T1302361922970000/290192 | altLabel | ef:agent/strip_catalogue_altlabels | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v16 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v17 |
| ef:activity/change/20260821T1302361922970000/322652 | concept_associations | ef:agent/carry_associations_onto_flows | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v17 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v18 |
| ef:activity/change/20260821T1302361922970000/391774 | properties | ef:agent/normalise_property_values | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v18 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v19 |
| ef:activity/change/20260821T1302361922970000/399958 | types | ef:agent/link_flows_to_their_substance | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v19 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v20 |
| ef:activity/change/20260821T1302361922970000/399959 | properties | ef:agent/link_flows_to_their_substance | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v20 | ef:flow/4694bc86-12ab-47d7-adf4-95b8b60e7174/v21 |