update owl tag generation

config/transformon_foodon.json

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+{
+    "encodeur" : "sentence-transformers/all-MiniLM-L6-v2",
+    "threshold_similarity_tag_chunk" : 0.50,
+    "threshold_similarity_tag" : 0.80,
+    "batch_size" : 32,
+
+    "populate_owl_tag_embeddings" : {
+        "ontologies": {
+            "transformon_link" : {
+                "po2": {
+                    "filepath" : "data/ontology/TransformON_V6.0.ttl",
+                    "prefix": "http://opendata.inrae.fr/PO2/Ontology/TransformON/",
+                    "format": "turtle",
+                    "label" : "<http://www.w3.org/2004/02/skos/core#prefLabel>",
+                    "properties": ["<http://www.w3.org/2004/02/skos/core#definition>"]
+                }
+            },
+            "foodon_link" : {
+                "foodon": {
+                    "url": "https://github.com/FoodOntology/foodon/raw/refs/tags/v2024-07-12/foodon.owl",
+                    "prefix": "http://purl.obolibrary.org/obo/",
+                    "format": "xml",
+                    "label" : "<http://www.w3.org/2000/01/rdf-schema#label>",
+                    "properties": ["<http://purl.obolibrary.org/obo/IAO_0000115>"]
+                }
+            }
+        },
+        "debug_nb_terms_by_ontology" : -1
+    },
+    "populate_abstract_embeddings" : {
+        "abstracts_per_file" : 50,
+        "from_file" : {
+            "json_files" : [
+		        "data/abstracts/abstracts_food-function-2024-yali-ran.json"
+            ]
+        }
+    }
+}

data/abstracts/abstracts_Identification_and_Quantification_of_Glucosinolates.json

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+[
+    {
+        "title": "Identification and Quantification of Glucosinolates and Phenolics in a Large Panel of Brassica napus Highlight Valuable Genetic Resources for Chemical Ecology and Breeding",
+        "abstract": "Glucosinolate (GLS) and phenolic contents in Brassicaceae contribute to biotic and abiotic stress responses. Breeding crop accessions harboring agroecologically relevant metabolic profiles require a characterization of the chemical diversity in Brassica germplasm. This work investigates the diversity of specialized metabolites in 281 accessions of B. napus. First, an LC-HRMS2-based approach allowed the annotation of 32 phenolics and 36 GLSs, revealing 13 branched and linear alkyl-GLSs and 4 isomers of hydroxyphenylalkyl-GLSs, many of which have been rarely reported in Brassica. Then, quantitative UPLC-UV-MS-based profiling was performed in leaves and roots for the whole panel. This revealed striking variations in the content of 1-methylpropyl-GLS (glucocochlearin) and a large variation of tetra- and penta-glucosyl kaempferol derivatives among accessions. It also highlighted two main chemotypes related to sinapoyl-O-hexoside and kaempferol-O-trihexoside contents. By offering an unprecedented overview of the phytochemical diversity in B. napus, this work provides a useful resource for chemical ecology and breeding",
+        "doi": "10.1021/acs.jafc.1c08118"
+    }
+]

data/abstracts/abstracts_PMC11328170.json

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+[
+    {
+        "title": "Modulatory Effects of Lactobacillus paracasei-Fermented Turmeric on Metabolic Dysregulation and Gut Microbiota in High-Fat Diet-Induced Obesity in Mice",
+        "abstract": "Turmeric, derived from Curcuma longa, and Lactobacillus paracasei, a lactic acid bacteria, have been studied for their potential antiobesity effects. To date, the antiobesity effects of turmeric fermented with L. paracasei have not been sufficiently investigated. This study was conducted via oral administration of 5% L. paracasei-fermented (FT) and unfermented turmeric (UT) in diet over 16 weeks using high-fat diet (HFD)-induced obese C57BL/6J mice. Results showed that the curcuminoid content of turmeric decreased following fermentation. Furthermore, FT significantly suppressed weight gain and liver and visceral adipose tissue weight and reduced plasma metabolic parameters in both the UT and FT experimental groups. The effects of FT were more noticeable than those of the unfermented form. Moreover, FT downregulated the expression of adipogenesis, lipogenesis, and inflammatory-related protein, but upregulated liver β-oxidation protein SIRT 1, PPARα, and PGC-1α in perigonadal adipose tissue. Additionally, FT ameliorated insulin resistance by activating insulin receptor pathway protein expressions in visceral adipose tissues. FT also modulated gut microbiota composition, particularly in two beneficial bacteria, Akkermansia muciniphila and Desulfovibrio, as well as two short-chain fatty acid-producing bacteria: Muribaculum intestinale and Deltaproteobacteria. Our findings indicate that the modulation effect of FT may be an important pathway for its antiobesity mechanisms.",
+        "doi": "10.1021/acs.jafc.4c01501"
+    }
+]

data/abstracts/abstracts_PMC11406343.json

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+[
+    {
+        "title": "Effect of different nitrogen source and Saccharomyces cerevisiae strain on volatile sulfur compounds and their sensory effects in chardonnay wine",
+        "abstract": "Three commercial Saccharomyces cerevisiae strains with low, medium, and high H2S-producing capacity were chosen to investigate the effect of yeast assimilable nitrogen (YAN) levels and composition on volatile compounds in a chemically defined medium, specifically high, medium, and low initial YAN levels with varying proportions of DAP or sulfur-containing amino acids (cysteine and methionine). The results revealed that the initial YAN containing a larger proportion of diammonium phosphate resulted in a higher YAN consumption rate during the early stages of fermentation. The yeast strain had a greater effect on the volatiles than the YAN level and composition. Keeping the total YAN constant, a higher proportion of sulfur-containing amino acids resulted in a considerably higher production of 3-methylthiopropanol. The sensory impact of three key volatile sulfur compounds was investigated in a Chardonnay wine matrix, indicating that 3-methylthiopropanol at subthreshold or greater concentrations was effective in enhancing the cantaloupe aroma.",
+        "doi": "10.1016/j.fochx.2024.101793"
+    }
+]

data/abstracts/abstracts_food-function-2024-yali-ran.json

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+[
+    {
+        "title": "Recent advances in dietary polyphenols (DPs): antioxidant activities, nutrient interactions, delivery systems, and potential applications",
+        "abstract": "Dietary polyphenols (DPs) have garnered growing interest because of their potent functional properties and health benefits. Nevertheless, the antioxidant capabilities of these substances are compromised by their multifarious structural compositions. Furthermore, most DPs are hydrophobic and unstable when subjected to light, heat, and varying pH conditions, restricting their practical application. Delivery systems based on the interactions of DPs with food constituents such as proteins, polypeptides, polysaccharides, and metal ions are being created as a viable option to improve the functional activities and bioavailability of DPs. In this review, the latest discoveries on the dietary sources, structure–antioxidant activity relationships, and interactions with nutrients of DPs are discussed. It also innovatively highlights the application progress of polyphenols and their green nutraceutical delivery systems. The conclusion drawn is that the various action sites and structures of DPs are beneficial for predicting and designing polyphenols with enhanced antioxidant attributes. The metal complexation of polyphenols and green encapsulation systems display promising outcomes for stabilizing DPs during food processing and in vivo digestion. In the future, more novel targeted delivery systems of DPs for nutrient fortification and intervention should be developed. To expand their usage in customized food products, they should meet the requirements of specific populations for personalized food and nutrition.",
+        "doi": "10.1039/D4FO02111H"
+    }
+]

data/abstracts/abstracts_lotus_natural_product_LTS0080835.json

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+[
+    {
+        "title": "Biologically Active Secondary Metabolites from Ginkgo biloba",
+        "abstract": "Three new compounds, (7E)-2β,3α-dihydroxy-megastigm-7-en-9-one (1), 3-[5,7-dihydroxy-2-(4-methoxyphenyl)-4-oxo-4H-chromen-8-yl]-4-methoxybenzoic acid (2), and 4‘-O-methyl myricetin 3-O-(6-O-α-l-rhamnopyranosyl)-β-d-glucopyranoside (3), were isolated from Ginkgo biloba, together with 27 known compounds. The structures of the new compounds were determined primarily from 1D- and 2D-NMR analysis. The 4-O-methylbenzoic acid structural feature at C-8 in 2 is encountered for the first time. The antioxidant activities of 29 compounds isolated from Ginkgo biloba were evaluated on intracellular reactive oxygen species in HL-60 cells. It was found that quercetin, kampferol, and tamarixetin had antioxidant activity that was approximately 3-fold greater than that of their respective glycosides and also approximately 3-fold greater than that of a standard ascorbic acid with an IC50 at maximum effectiveness.",
+        "doi": "10.1021/jf011682s"
+    }
+]

data/abstracts/abstracts_lotus_natural_product_LTS0137374.json

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+[
+    {
+        "title": "Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry of Solanidine, Leptinidine, and Acetylleptinidine. Steroidal Alkaloids from Solanum chacoense Bitter",
+        "abstract": "Solanidine, leptinidine, and acetylleptinidine from Solanum chacoense Bitter were structurally characterized by high-resolution MS and high-field 1H-NMR and 13C-NMR. 1H-NMR and 13C-NMR chemical shifts were assigned for solanidine and acetylleptinidine using DEPT, HMBC, and HMQC. Complete carbon chemical shift assignments are presented for all three alkaloids. The orientation of the C-23 acetoxyl group of acetylleptinidine was determined to be axial.",
+        "doi": "10.1021/jf9702914"
+    }
+]