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ASCT+B Validation Reports for Eye (2024-11-20)

Table of contents

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.

  1. The term UBERON:0000965 has a different name/label in the source ontology in the following 2 rows 59, 59. The name/label in the ASCT+B table is lens and the one in the ontology is lens of camera-type eye. For reference, the given name/label by SMEs is lens. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  2. The term UBERON:0004904 has a different name/label in the source ontology in the following 2 rows 70, 70. The name/label in the ASCT+B table is optic nerve and the one in the ontology is neuron projection bundle connecting eye with brain. For reference, the given name/label by SMEs is neuron projection bundle connecting eye with brain. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

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.

  1. No term id was found for the name/label glutamic acid decarboxylase 65 cell in the following 1 row 13.

  2. No term id was found for the name/label A8 bistratified small-field cell in the following 1 row 14.

  3. No term id was found for the name/label polyaxonal amacrine cell in the following 3 rows 16, 17, 18.

  4. No term id was found for the name/label semilunar type 1 cell in the following 1 row 16.

  5. No term id was found for the name/label semilunar type 3 cell in the following 1 row 17.

  6. No term id was found for the name/label semilunar cell in the following 1 row 18.

  7. No term id was found for the name/label Inner cortex in the following 1 row 46.

  8. No term id was found for the name/label Outer cortex in the following 2 rows 47, 53.

  9. No term id was found for the name/label conjuctival epithelium in the following 1 row 73.

  10. No term id was found for the name/label limbal stem cells in the following 1 row 74.

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.

  1. The term semilunar type 1 cell without ontology ID has no parent that is from the CL ontology in the following 1 row 16.

  2. The term semilunar type 3 cell without ontology ID has no parent that is from the CL ontology in the following 1 row 17.

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
3 UBERON:0034713 cranial neuron projection bundle nerve bundle UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve 68 28.0528
5 UBERON:0003902 retinal neural layer retinal neural layer UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve 67 20.494
7 UBERON:0001773 sclera sclera UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve 66 11.8988
13 UBERON:0000482 basal lamina of epithelium basal epithelium UBERON:0006761 corneo-scleral junction corneoscleral limbus 74 2.21739
19 UBERON:0002203 vasculature of eye vasculature of eye UBERON:0000966 retina retina 32 nan
32 UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve UBERON:0000970 eye eye 64 nan
33 UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve UBERON:0000970 eye eye 65 nan
34 UBERON:0035966 scleral lamina cribrosa scleral lamina cribrosa UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve 65 nan
35 UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve UBERON:0000970 eye eye 66 nan
36 UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve UBERON:0000970 eye eye 67 nan
37 UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve UBERON:0000970 eye eye 68 nan
38 UBERON:0004904 neuron projection bundle connecting eye with brain neuron projection bundle connecting eye with brain UBERON:0000970 eye eye 70 nan
39 UBERON:0006136 unmyelinated nerve fiber unmyelinated nerve bundles UBERON:0004904 neuron projection bundle connecting eye with brain neuron projection bundle connecting eye with brain 70 nan
40 UBERON:0002276 lamina of spiral limbus lamina of spiral limbus UBERON:0000970 eye eye 74 nan
41 UBERON:0006761 corneo-scleral junction corneoscleral limbus UBERON:0002276 lamina of spiral limbus lamina of spiral limbus 74 nan
42 UBERON:0000054 macula macula UBERON:0000966 retina retina 75 nan
43 UBERON:0018107 foveola of retina foveola of retina UBERON:0000054 macula macula 75 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.

s slabel user_slabel o olabel user_olabel row_number deltaIC
4 CL:0011005 GABAergic interneuron GABAergic interneuron CL:0000561 Amacrine Cell Amacrine cell 13 27.1717
15 CL:0004253 wide field retinal amacrine cell wide field cell CL:0004252 medium field retinal amacrine cell medium-field cell 15 nan
25 CL:0000129 microglial cell microglial cell CL:0000540 neuron Neuron 48 nan
27 CL:0000636 Mueller cell Muller glia CL:0000540 neuron Neuron 49 nan

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.

s slabel user_slabel o olabel user_olabel row_number deltaIC
0 CL:0000125 glial cell glial cell UBERON:0035966 scleral lamina cribrosa scleral lamina cribrosa 65 49.0237
1 CL:0000125 glial cell glial cell UBERON:0018107 foveola of retina foveola of retina 75 49.0237
2 CL:0000125 glial cell glial cell UBERON:0004904 neuron projection bundle connecting eye with brain optic nerve 64 32.6479
6 CL:0000036 epithelial fate stem cell epithelial fate stem cell UBERON:0000482 basal lamina of epithelium basal epithelium 74 19.1
8 CL:0000573 retinal cone cell retinal cone cell UBERON:0001789 outer nuclear layer of retina outer nuclear layer 33 10.8225
9 CL:0000604 retinal rod cell retinal rod cell UBERON:0001789 outer nuclear layer of retina outer nuclear layer 51 6.66658
10 CL:0011004 lens fiber cell lens fiber cell UBERON:0000390 lens nucleus Adult nucleus 45 6.03847
11 CL:0011004 lens fiber cell lens fiber cell UBERON:0000389 lens cortex cortex 46 4.56793
12 CL:0011004 lens fiber cell lens fiber cell UBERON:0000389 lens cortex cortex 47 4.56793
14 CL:4030028 glycinergic amacrine cell Glycinergic Amacrine Cell UBERON:0001791 inner nuclear layer of retina inner nuclear layer 14 nan
16 CL:0004253 wide field retinal amacrine cell wide field cell UBERON:0001791 inner nuclear layer of retina inner nuclear layer 15 nan
17 CL:0004219 A2 amacrine cell A2 cell UBERON:0001791 inner nuclear layer of retina inner nuclear layer 18 nan
18 CL:0004232 starburst amacrine cell starburst amacrine cell UBERON:0001791 inner nuclear layer of retina inner nuclear layer 19 nan
20 CL:0002585 retinal blood vessel endothelial cell Endothelial Cell UBERON:0004864 vasculature of retina vasculature 34 nan
21 CL:4023188 Midget ganglion cell of retina Midget cell UBERON:0001792 ganglionic layer of retina retinal ganglion cell layer 35 nan
22 CL:4023189 Parasol ganglion cell of retina Parasol cell UBERON:0001792 ganglionic layer of retina retinal ganglion cell layer 36 nan
23 CL:0002228 primary lens fiber primary lens fiber UBERON:0002444 lens fiber lens Fibers 38 nan
24 CL:0002225 secondary lens fiber mature fiber cell UBERON:0000390 lens nucleus Fetal nucleus 44 nan
26 CL:0000129 microglial cell microglial cell UBERON:0000966 retina retina 48 nan
28 CL:0000636 Mueller cell Muller glia UBERON:0001791 inner nuclear layer of retina inner nuclear layer 49 nan
29 CL:0000669 pericyte Pericyte UBERON:0004864 vasculature of retina vasculature 50 nan
30 CL:0002363 keratocyte keratocyte UBERON:0003952 anterior stroma of cornea anterior stroma of cornea 56 nan
31 CL:0017004 telocyte telocyte UBERON:0003952 anterior stroma of cornea anterior stroma of cornea 57 nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report