Consider Removing Retracted Papers from RTX-KG2

[ecwood]

There are currently retracted papers that show up in the publications field of edges in RTX-KG2pre (checking against KG2.9.0). While these are just two examples, it is likely that there are many others in RTX-KG2:. (These were manually identified, by looking up major scientific retractions and searching for them in RTX-KG2.) Further, while their results may not seem significant, it is difficult to know the full extent of damage done by retracted papers in RTX-KG2 without significant investment.

• The Vaccines Cause Autism Paper: PMID:9500320 (Wakefield AJ, Murch SH, Anthony A, Linnell J, Casson DM, Malik M, Berelowitz M, Dhillon AP, Thomson MA, Harvey P, Valentine A, Davies SE, Walker-Smith JA. Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. Lancet. 1998 Feb 28;351(9103):637-41. doi: 10.1016/s0140-6736(97)11096-0. Retraction in: Lancet. 2010 Feb 6;375(9713):445. doi: 10.1016/S0140-6736(10)60175-4. Erratum in: Lancet. 2004 Mar 6;363(9411):750. doi: 10.1016/S0140-6736(04)15715-2. PMID: 9500320.)

match (n)-[e]->(m) where "PMID:9500320" in e.publications return n.name, n.id, e.predicate, m.name, m.id limit 50

n.name	n.id	e.predicate	m.name	m.id
"Hemoglobin"	"UMLS:C0019046"	"biolink:located_in"	"child"	"UMLS:C0008059"
"CD79A"	"NCBIGene:973"	"biolink:located_in"	"child"	"UMLS:C0008059"
"(non-specific) colitis"	"UMLS:C1321275"	"biolink:occurs_in"	"child"	"UMLS:C0008059"
"Lymphoid hyperplasia"	"UMLS:C0333997"	"biolink:occurs_in"	"child"	"UMLS:C0008059"
"Measles"	"UMLS:C0025007"	"biolink:occurs_in"	"Parent"	"UMLS:C0030551"
"Pseudolymphoma"	"UMLS:C0221269"	"biolink:located_in"	"ileum"	"UMLS:C0020885"
"barium follow through"	"UMLS:C0412113"	"biolink:subclass_of"	"Diagnostic radiologic examination"	"UMLS:C0043299"
"Chronic inflammation"	"UMLS:C0021376"	"biolink:located_in"	"Colon structure (body structure)"	"UMLS:C0009368"
"CD79A"	"NCBIGene:973"	"biolink:located_in"	"Serum"	"UMLS:C0229671"
"Hemoglobin"	"UMLS:C0019046"	"biolink:related_to"	"CD79A"	"NCBIGene:973"
"Hemoglobin"	"UMLS:C0019046"	"biolink:related_to"	"LOC102723407"	"NCBIGene:102723407"

• PMID:9492007 (Van Parijs L, Peterson DA, Abbas AK. The Fas/Fas ligand pathway and Bcl-2 regulate T cell responses to model self and foreign antigens. Immunity. 1998 Feb;8(2):265-74. doi: 10.1016/s1074-7613(00)80478-1. Retraction in: Immunity. 2009 Apr 17;30(4):611. doi: 10.1016/j.immuni.2009.04.001. PMID: 9492007.)

match (n)-[e]->(m) where "PMID:9492007" in e.publications return n.name, n.id, e.predicate, m.name, m.id limit 50

n.name	n.id	e.predicate	m.name	m.id
"lysozyme, chicken egg white"	"UMLS:C0964782"	"biolink:produces"	"Autoantigens"	"UMLS:C0004359"
"lysozyme, chicken egg white"	"UMLS:C0964782"	"biolink:related_to"	"Cells"	"UMLS:C0007634"
"Autoantigens"	"UMLS:C0004359"	"biolink:affects"	"lysozyme, chicken egg white"	"UMLS:C0964782"

Retraction Watch is now publicly available for download. We should consider including them as a source, to remove edges that cite them. (See https://www.crossref.org/blog/news-crossref-and-retraction-watch/ about download)