--label
"MeSH-2022" --eliminate-redundancy. It produces following errors and failed to output TTL file -
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#AllowedDescriptorQualifierPair
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#CheckTag
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#Concept
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#DisallowedDescriptorQualifierPair
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#GeographicalDescriptor
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#PublicationType
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#Qualifier
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#SCR_Chemical
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#SCR_Disease
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#SCR_Organism
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#SCR_Protocol
INFO:
Don't know what to do with type http://id.nlm.nih.gov/mesh/vocab#Term
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#TopicalDescriptor
INFO:
Don't know what to do with type
http://id.nlm.nih.gov/mesh/vocab#TreeNumber
INFO:
No skos:ConceptScheme or owl:Ontology found. Using namespace
auto-detection for creating concept scheme.
CRITICAL:
Namespace auto-detection failed. Set namespace using the --namespace
option.
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Actually, we could loadvoc MeSH ttl file in Annif after the initial hiccup with the memory issue, but it has never worked for our training dataset made by using Pubmed. Now, I understand the reason.
We tried to solve this issue by creating a subject key file in tsv format on the basis of Pubmed xml download (https://www.nlm.nih.gov/databases/download/pubmed_medline.html) treated in OpenRefine like
<http://id.nlm.nih.gov/mesh/D000255> | Adenosine Triphosphate |
<http://id.nlm.nih.gov/mesh/D000273> | Adipose Tissue |
<http://id.nlm.nih.gov/mesh/D000317> | Adrenergic alpha-Antagonists |
<http://id.nlm.nih.gov/mesh/D000319> | Adrenergic beta-Antagonists |
<http://id.nlm.nih.gov/mesh/D000818> | Animals |
<http://id.nlm.nih.gov/mesh/D004837> | Epinephrine |
<http://id.nlm.nih.gov/mesh/D006593> | Hexokinase |
<http://id.nlm.nih.gov/mesh/D066298> | In Vitro Techniques |
<http://id.nlm.nih.gov/mesh/D008156> | Luciferases |
......
Then we trained the mesh project with 3 million dataset (as a test case). The pilot project is working for us by following the above methodology.
Today, we've tried the mesh ttl as pointed out by you. But we need to change one statement in the tll file from @prefix mesh: <http://www.yso.fi/onto/mesh/> . to @prefix mesh: <http://id.nlm.nih.gov/mesh/> .
as our training dataset format is like -
[Biochemical studies on camomile components/III. In vitro studies about the antipeptic activity of (--)-alpha-bisabolol (author's transl)]. ¤ (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol only occurs in case of direct contact. In case of a previous contact with the substrate, the inhibiting effect is lost. | <http://id.nlm.nih.gov/mesh/D004305> <http://id.nlm.nih.gov/mesh/D006454> <http://id.nlm.nih.gov/mesh/D006863> <http://id.nlm.nih.gov/mesh/D066298> <http://id.nlm.nih.gov/mesh/D008722> <http://id.nlm.nih.gov/mesh/D010434> <http://id.nlm.nih.gov/mesh/D010946> <http://id.nlm.nih.gov/mesh/D012717> <http://id.nlm.nih.gov/mesh/D013056> <http://id.nlm.nih.gov/mesh/D014238> <http://id.nlm.nih.gov/mesh/D014443> |
It's rocking now.
Thanks a lot.
Best regards
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