ASCT+B Validation Reports for Anatomical_Systems (2024-07-04)

Invalid terms

These are the reports related to issues in the terms found in the ASCT+B table. We validate only CL, UBERON and PCL terms.

Terms not found

This report provides a list of terms not found neither in UBERON nor in CL. Please remove these terms from the ASCT+B table - disconsider this message if a term was recently added to the ontology.

No issues found.

Typos or punctuation mistakes

This report provides a general quality check of the terms used in the ASCT+B table. Typos, font case (upper case), punctuation mistakes in IDs: two colons, spaces, underscore instead of a colon.

No issues found.

Different labels

This report provides a list of terms having different names/labels found in the ontology and related to the one found in the ASCT+B table. Make sure to add the term's name/label in the column AS/N/LABEL or CT/N/LABEL. If the SME wants to give another name/label, please use the column AS/N or CT/N. N is the number in the column.

If the term's name/label and the name/label given by SME are too different, please make sure the term ID and its name/label are matching in OLS.

If the name/label in the ontology contains obsolete, please look into OLS, clicking on the term ID, for its replacement.

No issues found.

Blank ontology ID

This report provides a list of blank spreadsheet cells that often mean no ontology mapping found by the author. However, in some cases, a term with a synonym already exists. Please search in OLS.

You can find more information on the New CL terms or New UBERON terms reports.

No issues found.

Blank ontology ID missing parent

This report provides a list of CT terms with blank ontology ID without an upper term from Cell Ontology. Please, create an upper level in the ASCT+B table and add an upper term for them. Please, make sure the term without ontology ID doesn't exist in the ontology.

No issues found.

Terms from another ontology

This report provides a list of terms from another ontologies that we do not validate. Foundational Model of Anatomy (FMA) ontology IDs are provided when an adequate term is not found in UBERON. Same case for Anatomic Ontology for Human Lung Maturation (LMHA) and Interlex IDs (ILX) from Stimulating Peripheral Activity to Relieve Conditions (SPARC). You can request cross-database request the same way a new term request. Please be sure if a term with a related synonym is already in the source ontologies CL or UBERON or PCL.

No issues found.

Relationship reports

These reports are other representations of the ASCT+B table. We split each row into pairs with adjacent terms, resulting in a table with two primary columns, object (o), left side and subject (s), right side. The experts' labels for the subject and object are in the columns user_slabel and user_olabel. The other columns are the subject label (s_label) and object label (o_label), the label from the source ontologies.

The report means it could not find a partonomy relationship in the source ontologies, but it doesn't mean this relationship is entirely invalid. In some cases, the pair is in the inverse order. In other cases, the relationship is missing in the source ontologies. Finally, how it was modelled in the ASCT+B table is not aligned with the ontologies sources and needs a more general discussion.

How to read a table entry

In the ASCT+B table

AS/2	AS/2/LABEL	AS/2/ID	AS/3	AS/3/LABEL	AS/3/ID
lens	lens	UBERON:0000965	ciliary zonules	suspensory ligament of lens	UBERON:0006762

In the Relationship Report

s	slabel	user_slabel	o	olabel	user_olabel
UBERON:0006762	suspensory ligament of lens	ciliary zonules	UBERON:0000965	lens	lens

Relationship AS-AS report

This table contains terms for anatomical structures that are related to each other according to the ASCT+B table but are not related to each other in source ontologies via one of the relation types we consider valid for ASCT+B tables. Valid relationships are: part_of, e.g. corneal endothelium part_of cornea; subClassOf, e.g. left kidney subClassOf (is_a) kidney; and overlaps (has some part in), e.g. ureter overlaps kidney; connected_to, e.g. TBA. part_of and subClassOf relationships should be specific to general, e.g. left kidney (specific) to kidney (general); corneal endothelium (specific) to cornea (general). The deltaIC score is included because a high score (>50) can indicate that this order is reversed, e.g. TBA.

	s	slabel	user_slabel	o	olabel	user_olabel	row_number	deltaIC
0	UBERON:0002405	immune system	immune system	UBERON:0000467	anatomical system	anatomical system	24	nan
1	UBERON:0002405	immune system	immune system	UBERON:0000467	anatomical system	anatomical system	25	nan
2	UBERON:0002405	immune system	immune system	UBERON:0000467	anatomical system	anatomical system	26	nan
3	UBERON:0002405	immune system	immune system	UBERON:0000467	anatomical system	anatomical system	27	nan
4	UBERON:0002405	immune system	immune system	UBERON:0000467	anatomical system	anatomical system	28	nan
5	UBERON:0002405	immune system	immune system	UBERON:0000467	anatomical system	anatomical system	29	nan
6	UBERON:0004175	internal genitalia	internal genitalia	UBERON:0000474	female reproductive system	female reproductive system	45	nan
7	UBERON:0004175	internal genitalia	internal genitalia	UBERON:0000474	female reproductive system	female reproductive system	46	nan

Relationship CT-CT report

In the case of the CT-CT relationship, for each couple of terms, we verify for sub class of, part of and overlaps in the source ontologies. The deltaIC score is included because a high score (>50) can indicate that this order is reversed, e.g. TBA.

No issues found.

Relationship CT-AS report

In the case of the AS-CT relationship, for each couple of terms, we verify for connected to and has part in the source ontologies.

ASCT+B Validation Reports for Anatomical_Systems (2024-07-04)

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