Skip to content

fix: remove prefix.cc spam and stop refreshing prefix.cc by default #86

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
kevinschaper merged 3 commits into from
Nov 6, 2026
Merged

fix: remove prefix.cc spam and stop refreshing prefix.cc by default #86

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
c2941ba
fix: remove prefix.cc spam and block it from coming back
jdsika Oct 21, 2026
3bd0f24
feat: stop refreshing prefix.cc by default
jdsika Oct 21, 2026
65c1495
Merge branch 'main' into fix/prefixcc-spam
kevinschaper Nov 6, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,8 @@ converter = load_converter("obo", refresh=True)

This will perform a fetch from http://obofoundry.org/registry/obo_prefixes.ttl

prefix.cc is the exception: `refresh=True` still uses the bundled prefix.cc data, because prefix.cc is not curated (see [Refreshing the Data](#refreshing-the-data)).

## Context Metadata

See [contexts.curated.yaml](src/prefixmaps/data/contexts.curated.yaml)
Expand Down Expand Up @@ -172,6 +174,11 @@ The data can be refreshed in several ways:
make etl
```

prefix.cc is not refreshed by default, because it has no curation and spam keeps reappearing there (see [#61](https://github.com/linkml/prefixmaps/issues/61)).
To fix a semantic web prefix, add it to [linked_data.curated.yaml](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/linked_data.curated.yaml), which takes precedence over prefix.cc in the merged contexts.
To download prefix.cc anyway, run `slurp-prefixmaps --refresh-prefixcc`, and review the rows it prints and the resulting CSV diff before committing.
prefix.cc entries that must never be imported are listed in [prefixcc.excluded.yaml](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/prefixcc.excluded.yaml).

TODO: make a github action that auto-releases new versions

Note that PRs should *not* be made against the individual CSV files. These are generated from upstream sources.
Expand Down
7 changes: 7 additions & 0 deletions docs/intro.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -126,6 +126,8 @@ ctxt = load_context("obo", refresh=True)

This will perform a fetch from http://obofoundry.org/registry/obo_prefixes.ttl

prefix.cc is the exception: `refresh=True` still uses the bundled prefix.cc data, because prefix.cc is not curated.

## Context Metadata

See [contexts.curated.yaml](src/prefixmaps/data/contexts.curated.yaml)
Expand All @@ -146,6 +148,11 @@ These can be regenerated using:
make etl
```

prefix.cc is not refreshed by default, because it has no curation and spam keeps reappearing there.
To fix a semantic web prefix, add it to `linked_data.curated.yaml`, which takes precedence over prefix.cc in the merged contexts.
To download prefix.cc anyway, run `slurp-prefixmaps --refresh-prefixcc`, and review the rows it prints and the resulting CSV diff before committing.
prefix.cc entries that must never be imported are listed in `prefixcc.excluded.yaml`.

TODO: make a github action that auto-released new versions

## Requesting new prefixes
Expand Down
15 changes: 0 additions & 15 deletions src/prefixmaps/data/merged.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -936,7 +936,6 @@ merged,BFO,http://www.ebi.ac.uk/ols/ontologies/bfo/terms?iri=http://purl.obolibr
merged,BFO,https://bioregistry.io/BFO:,prefix_alias,bioregistry
merged,BFO,https://purl.obolibrary.org/obo/BFO_,prefix_alias,bioregistry
merged,BFO,https://www.ebi.ac.uk/ols/ontologies/bfo/terms?iri=http://purl.obolibrary.org/obo/BFO_,prefix_alias,bioregistry
merged,bgcat,http://bg.dbpedia.org/resource/?????????:,canonical,prefixcc
merged,bgdbp,http://bg.dbpedia.org/property/,canonical,prefixcc
merged,bgdbr,http://bg.dbpedia.org/resource/,canonical,prefixcc
merged,BGEE.FAMILY,http://identifiers.org/bgee.family/,canonical,bioregistry
Expand Down Expand Up @@ -1972,7 +1971,6 @@ merged,CHEBI,https://www.ebi.ac.uk/chebi/searchId.do?chebiId=,prefix_alias,biore
merged,CHEBI,https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:,prefix_alias,bioregistry
merged,CHEBI,https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http://purl.obolibrary.org/obo/CHEBI_,prefix_alias,bioregistry
merged,CHEBIID,http://purl.obolibrary.org/obo/CHEBI_,namespace_alias,bioregistry
merged,check,http://pornhub.com/,canonical,prefixcc
merged,checks,https://data.digichecks.eu/def/,canonical,prefixcc
merged,CHEMBL,http://identifiers.org/chembl/,canonical,bioregistry
merged,CHEMBL,http://bio2rdf.org/chembl:,prefix_alias,bioregistry
Expand Down Expand Up @@ -3547,7 +3545,6 @@ merged,DHBA,https://bioregistry.io/DHBA:,prefix_alias,bioregistry
merged,DI,https://www.uniprot.org/diseases/,namespace_alias,bioregistry
merged,diag,http://www.loc.gov/zing/srw/diagnostic/,canonical,prefixcc
merged,dicera,http://semweb.mmlab.be/ns/dicera#,canonical,prefixcc
merged,dick,http://pornhub.com/,namespace_alias,prefixcc
merged,DICOM,http://dicom.nema.org/resources/ontology/DCM/,canonical,bioregistry
merged,DICOM,http://bioregistry.io/dicom:,prefix_alias,bioregistry
merged,DICOM,https://bioregistry.io/dicom:,prefix_alias,bioregistry
Expand Down Expand Up @@ -4946,7 +4943,6 @@ merged,FAO.ASFIS,http://www.fao.org/fishery/en/species/,prefix_alias,bioregistry
merged,FAO.ASFIS,https://bioregistry.io/asfis:,prefix_alias,bioregistry
merged,FAO.ASFIS,https://bioregistry.io/fao.asfis:,prefix_alias,bioregistry
merged,faostat,http://reference.eionet.europa.eu/faostat/schema/,canonical,prefixcc
merged,faptica,https://faptica.com/,canonical,prefixcc
merged,faq,http://www.openlinksw.com/ontology/faq#,canonical,prefixcc
merged,FB,http://identifiers.org/flybase/,canonical,go
merged,FBbi,http://purl.obolibrary.org/obo/FBbi_,canonical,obo
Expand Down Expand Up @@ -5261,7 +5257,6 @@ merged,friends,http://www.openarchives.org/OAI/2.0/friends/,canonical,prefixcc
merged,frir,http://purl.org/twc/ontology/frir.owl#,canonical,prefixcc
merged,fro,https://foundry.ai.mil/ontology/nas/fro/,canonical,prefixcc
merged,frsad,http://iflastandards.info/ns/fr/frsad/,canonical,prefixcc
merged,fs,https://www.compliancequest.com/training-management-software-system-solutions/,canonical,prefixcc
merged,FSNP,http://identifiers.org/fsnp/,canonical,bioregistry
merged,FSNP,http://bio2rdf.org/fsnp:,prefix_alias,bioregistry
merged,FSNP,http://bioregistry.io/fsnp:,prefix_alias,bioregistry
Expand All @@ -5279,7 +5274,6 @@ merged,fssp,http://linkeddata.fssprus.ru/resource/,canonical,prefixcc
merged,ftcontent,http://www.ft.com/ontology/content/,canonical,prefixcc
merged,fti,http://franz.com/ns/allegrograph/2.2/textindex/,canonical,prefixcc
merged,ftr,https://w3id.org/ftr#,canonical,prefixcc
merged,fugas,https://onlyfans.com/sammuwuu/,canonical,prefixcc
merged,fun,http://w3id.org/sparql-generate/fn/,canonical,prefixcc
merged,func,http://www.w3.org/2007/rif-builtin-function#,canonical,prefixcc
merged,FUNCBASE.FLY,http://identifiers.org/funcbase.fly/,canonical,bioregistry
Expand Down Expand Up @@ -8049,7 +8043,6 @@ merged,lds,https://solid.ti.rw.fau.de/public/ns/linked-data-structures#,canonica
merged,ldt,https://www.w3.org/ns/ldt#,canonical,prefixcc
merged,ldvm,http://linked.opendata.cz/ontology/ldvm/,canonical,prefixcc
merged,leak,http://maco.com/,canonical,prefixcc
merged,leaks,https://onlyfans.com/chelxie/,canonical,prefixcc
merged,led,http://led.kmi.open.ac.uk/term/,canonical,prefixcc
merged,legal,http://www.w3.org/ns/legal#,canonical,prefixcc
merged,LEI,http://identifiers.org/lei/,canonical,bioregistry
Expand Down Expand Up @@ -8285,7 +8278,6 @@ merged,lis,http://rds.posccaesar.org/ontology/lis14/rdl/,canonical,prefixcc
merged,list,http://www.w3.org/2000/10/swap/list#,canonical,prefixcc
merged,literal,http://www.essepuntato.it/2010/06/literalreification/,canonical,prefixcc
merged,literature,http://purl.org/net/cnyt-literature#,canonical,prefixcc
merged,ljkl,http://teste.com/,canonical,prefixcc
merged,ll,http://lodlaundromat.org/resource/,canonical,prefixcc
merged,llalg,http://www.linklion.org/algorithm/,canonical,prefixcc
merged,lldr,http://purl.oclc.org/NET/lldr/ns#,canonical,prefixcc
Expand Down Expand Up @@ -11152,7 +11144,6 @@ merged,ONE,https://purl.obolibrary.org/obo/ONE_,prefix_alias,bioregistry
merged,ONE,https://www.ebi.ac.uk/ols/ontologies/one/terms?iri=http://purl.obolibrary.org/obo/ONE_,prefix_alias,bioregistry
merged,one,https://bioportal.bioontology.org/ontologies/ONE/,prefix_alias,prefixcc
merged,onisep,http://rdf.onisep.fr/resource/,canonical,prefixcc
merged,onlyfans,https://cutt.ly/3ry8LMcK/,canonical,prefixcc
merged,ONS,http://purl.obolibrary.org/obo/ONS_,canonical,obo
merged,ONS,http://bioregistry.io/ONS:,prefix_alias,bioregistry
merged,ONS,http://www.ebi.ac.uk/ols/ontologies/ons/terms?iri=http://purl.obolibrary.org/obo/ONS_,prefix_alias,bioregistry
Expand Down Expand Up @@ -12774,7 +12765,6 @@ merged,prviv,http://purl.org/net/provenance/integrity#,canonical,prefixcc
merged,prvr,http://purl.org/ontology/prv/rules#,canonical,prefixcc
merged,prvt,http://purl.org/net/provenance/types#,namespace_alias,prefixcc
merged,prvtypes,http://purl.org/net/provenance/types#,canonical,prefixcc
merged,przecieki,http://onlyfans.com/emiliaszymanska/,canonical,prefixcc
merged,ps,https://w3id.org/payswarm#,canonical,prefixcc
merged,PSCDB,http://identifiers.org/pscdb/,canonical,bioregistry
merged,PSCDB,http://bioregistry.io/pscdb:,prefix_alias,bioregistry
Expand Down Expand Up @@ -13091,7 +13081,6 @@ merged,QTLDB,https://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=,pref
merged,QTLDB,https://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=,prefix_alias,bioregistry
merged,qu,http://purl.oclc.org/NET/ssnx/qu/qu#,canonical,prefixcc
merged,quak,http://dev.w3.org/cvsweb/2000/quacken/vocab#,canonical,prefixcc
merged,qualityze,https://www.qualityze.com/document-management/,canonical,prefixcc
merged,quantities,http://eulersharp.sourceforge.net/2003/03swap/quantitiesExtension#,canonical,prefixcc
merged,quantity,http://qudt.org/schema/quantity#,canonical,prefixcc
merged,qud,http://qudt.org/1.1/schema/qudt#,namespace_alias,prefixcc
Expand Down Expand Up @@ -13130,7 +13119,6 @@ merged,railml3,http://ontology.railml.org/railml3#,canonical,prefixcc
merged,rami,http://iais.fraunhofer.de/vocabs/rami#,canonical,prefixcc
merged,ramon,http://rdfdata.eionet.europa.eu/ramon/ontology/,canonical,prefixcc
merged,rank,http://www.ontotext.com/owlim/RDFRank#,canonical,prefixcc
merged,rankrage,https://rankrage.de/,canonical,prefixcc
merged,RAPDB.LOCUS,http://identifiers.org/rapdb.locus/,canonical,bioregistry
merged,RAPDB.LOCUS,http://bioregistry.io/irgsp:,prefix_alias,bioregistry
merged,RAPDB.LOCUS,http://bioregistry.io/rapdb.locus:,prefix_alias,bioregistry
Expand Down Expand Up @@ -14128,7 +14116,6 @@ merged,SEO,http://bioregistry.io/seo:,prefix_alias,bioregistry
merged,SEO,http://w3id.org/seo#,prefix_alias,bioregistry
merged,SEO,https://bioregistry.io/seo:,prefix_alias,bioregistry
merged,seo,http://sda.tech/SEOontology/SEO/,prefix_alias,prefixcc
merged,seokoeln,http://rankrage.de/,canonical,prefixcc
merged,SEP,http://purl.obolibrary.org/obo/SEP_,canonical,obo
merged,SEP,http://bio2rdf.org/sep:,prefix_alias,bioregistry
merged,SEP,http://bioregistry.io/SEP:,prefix_alias,bioregistry
Expand Down Expand Up @@ -15619,7 +15606,6 @@ merged,TXPO,http://www.ebi.ac.uk/ols/ontologies/txpo/terms?iri=http://purl.oboli
merged,TXPO,https://bioregistry.io/TXPO:,prefix_alias,bioregistry
merged,TXPO,https://purl.obolibrary.org/obo/TXPO_,prefix_alias,bioregistry
merged,TXPO,https://www.ebi.ac.uk/ols/ontologies/txpo/terms?iri=http://purl.obolibrary.org/obo/TXPO_,prefix_alias,bioregistry
merged,type,http://teste.com/teste/,canonical,prefixcc
merged,tzont,http://www.w3.org/2006/timezone#,canonical,prefixcc
merged,ub,http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl#,canonical,prefixcc
merged,ubbont,http://data.ub.uib.no/ontology/,canonical,prefixcc
Expand Down Expand Up @@ -16374,7 +16360,6 @@ merged,VECTORBASE,https://n2t.net/vectorbase:,prefix_alias,bioregistry
merged,VECTORBASE,https://vectorbase.org/gene/,prefix_alias,bioregistry
merged,VECTORBASE,https://vectorbase.org/vectorbase/app/record/gene/,prefix_alias,bioregistry
merged,VECTORBASE,https://www.vectorbase.org/[?species_name]/Gene/Summary?db=core;g=,prefix_alias,bioregistry
merged,veelana,http://onlyfans.com/veelana/,canonical,prefixcc
merged,VEGBANK,http://identifiers.org/vegbank/,canonical,bioregistry
merged,VEGBANK,http://bioregistry.io/vegbank:,prefix_alias,bioregistry
merged,VEGBANK,http://identifiers.org/vegbank:,prefix_alias,bioregistry
Expand Down
Loading
Loading