| {"application": "software-mentions", "version": "0.9.0-SNAPSHOT", "revision": "54efbc6", "date": "2026-10-14T14:56+0000", "md5": "E5EBFAA97C665A7860BB5553A7F518F1", "biblio": {"title": "Assessing bioinformatics software annotations: bio.tools case-study", "authors": "Ulysse Le Clanche, Sarah Cohen Boulakia, Yann Le Cunff, Olivier Dameron, Alban Gaignard"}, "mentions": [{"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 0, "offsetEnd": 4}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "EDAM.", "mentionContextAttributes": {"used": {"value": false, "score": 0.004689991474151611}, "created": {"value": false, "score": 0.001006782054901123}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 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"context": "bio.tools ), or analysis pipelines (e.g.", "mentionContextAttributes": {"used": {"value": false, "score": 0.010901689529418945}, "created": {"value": false, "score": 5.137920379638672e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": false, "score": 0.010901689529418945}, "created": {"value": false, "score": 0.0017705559730529785}, "shared": {"value": false, "score": 3.5762786865234375e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Work-flowHub", "normalizedForm": "Work-flowHub", "offsetStart": 0, "offsetEnd": 15}, "context": "Work-flowHub ).", "mentionContextAttributes": {"used": {"value": false, "score": 0.09371310472488403}, "created": {"value": false, "score": 3.0279159545898438e-05}, "shared": {"value": false, "score": 0.04045778512954712}}, "documentContextAttributes": {"used": {"value": false, "score": 0.09371310472488403}, "created": {"value": false, "score": 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"software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 4, "offsetEnd": 8}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "The EDAM hierarchy of terms helps to enrich assigned annotations for all tools, taking ancestors into account.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00037992000579833984}, "created": {"value": false, "score": 5.14984130859375e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 8, "offsetEnd": 12}, "version": {"rawForm": "1.25", "normalizedForm": "1.25", "offsetStart": 21, "offsetEnd": 25}, "context": "We used EDAM version 1.25, and focused only on Operation and Topic annotations, the most used annotations in bio.tools (100k+ topics, 70k+ operations, 11k+ data and 10k+ formats).", "mentionContextAttributes": {"used": {"value": true, "score": 0.9998385906219482}, "created": {"value": false, "score": 2.300739288330078e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "implicit", "software-name": {"rawForm": "code", "normalizedForm": "code", "offsetStart": 8, "offsetEnd": 12}, "url": {"rawForm": "https://github.com/ ulysseLeclanche/Abso_bio-tools", "normalizedForm": "https://github.com/ ulysseLeclanche/Abso_bio-tools", "offsetStart": 175, "offsetEnd": 227}, "context": "All the code for extracting metadata from the RDF schema, creating article figures and calculating tool annotation statistics is available on the following github repository: https://github.com/ ulysseLeclanche/Abso_bio-tools.", "mentionContextAttributes": {"used": {"value": false, "score": 0.292327344417572}, "created": {"value": false, "score": 0.0003114938735961914}, "shared": {"value": true, "score": 0.8668342232704163}}, "documentContextAttributes": {"used": {"value": false, "score": 0.292327344417572}, "created": {"value": false, "score": 0.0003114938735961914}, "shared": {"value": true, "score": 0.8668342232704163}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 8, "offsetEnd": 13}, "context": "The two tools share only one directly assigned annotation {Metagenomics}, accounting for 16% of all direct annotations, which is relatively low given their use in the same application domain.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0074024200439453125}, "created": {"value": false, "score": 1.2636184692382812e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 12, "offsetEnd": 17}, "context": "This set of tools should be prioritized for future database curation activities.", "mentionContextAttributes": {"used": {"value": false, "score": 4.7326087951660156e-05}, "created": {"value": false, "score": 0.06005781888961792}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Qiime2", "normalizedForm": "Qiime2", "offsetStart": 12, "offsetEnd": 23}, "context": "We selected Qiime2 and Vsearch as two reference bioinformatics tools used in metagenomics data analysis.", "mentionContextAttributes": {"used": {"value": true, "score": 0.7124571800231934}, "created": {"value": false, "score": 0.04206216335296631}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.7124571800231934}, "created": {"value": false, "score": 0.04206216335296631}, "shared": {"value": false, "score": 2.384185791015625e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 16, "offsetEnd": 20}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "Data and Format EDAM classes are not well instantiated (used) in the bio.tools registry, even though they are as important as Topic and Operation.", "mentionContextAttributes": {"used": {"value": false, "score": 0.001692056655883789}, "created": {"value": false, "score": 1.2278556823730469e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 20, "offsetEnd": 25}, "context": "TeSS [6]), software tools (e.g.", "mentionContextAttributes": {"used": {"value": false, "score": 0.035796940326690674}, "created": {"value": false, "score": 1.3709068298339844e-05}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 20, "offsetEnd": 25}, "context": "The distribution of tools with redundant annotations is similar in each group, with 2,369 (14.87%) redundant tools in the low information level, 2,193 (16.70%) in the medium level and 86 (8.92%) in the high level.", "mentionContextAttributes": {"used": {"value": false, "score": 0.04503864049911499}, "created": {"value": false, "score": 4.220008850097656e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 21, "offsetEnd": 26}, "context": "Unfortunately, fewer tools are annotated by elements from these branches (among the 30 025 annotated tools 98.64 % Topics, 94.25 % Operations, 9.64 % Formats, 12.95 % Datas).", "mentionContextAttributes": {"used": {"value": false, "score": 0.10308122634887695}, "created": {"value": false, "score": 7.3909759521484375e-06}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 24, "offsetEnd": 29}, "context": "We estimated that 3,405 tools (11.34%) have redundant direct topic annotations, and 2,055 tools (6.84%) have redundant direct operation annotations.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9992111921310425}, "created": {"value": false, "score": 4.649162292480469e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 24, "offsetEnd": 29}, "context": "However, if we take two tools with a similar number of annotations but different rarity in term annotation, the tool with the most rare terms will have a higher entropy.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0009725093841552734}, "created": {"value": false, "score": 3.457069396972656e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 25, "offsetEnd": 29}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "These registries rely on EDAM [9], an ontology aimed at improving interoperability in bioinformatics by formally defining the nature and format of data produced and managed, different kinds of data processing, as well as the associated scientific disciplines.", "mentionContextAttributes": {"used": {"value": false, "score": 0.006151258945465088}, "created": {"value": false, "score": 0.00016295909881591797}, "shared": {"value": false, "score": 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"software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 26, "offsetEnd": 31}, "context": "However, among the top 10 tools with the highest entropy sum, 60% of tools have redundant annotations.", "mentionContextAttributes": {"used": {"value": false, "score": 0.01235806941986084}, "created": {"value": false, "score": 2.193450927734375e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 27, "offsetEnd": 32}, "context": "This illustrates that some tools have few annotations, and have direct annotations with various levels of precision.", "mentionContextAttributes": {"used": {"value": false, "score": 9.059906005859375e-05}, "created": {"value": false, "score": 7.2479248046875e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 27, "offsetEnd": 32}, "context": "We computed the entropy of tools annotated with EDAM topics and operations.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": false, "score": 5.4001808166503906e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 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"mentionContextAttributes": {"used": {"value": false, "score": 0.02680104970932007}, "created": {"value": false, "score": 6.0677528381347656e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 31, "offsetEnd": 36}, "context": "We also computed the number of tools annotated with redundant EDAM classes.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9999940395355225}, "created": {"value": false, "score": 5.1975250244140625e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, 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"offsetEnd": 40}, "context": "To search and reuse bioinformatics tools, scientists need to be confident enough with the reliability of their annotations.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0002078413963317871}, "created": {"value": false, "score": 0.00014865398406982422}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 38, "offsetEnd": 43}, "context": "Although this work is grounded to bio.tools, it aims at being generalized to other application domains also using ontologies and registries for annotating and sharing FAIR digital resources.", "mentionContextAttributes": {"used": {"value": false, "score": 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"tools", "normalizedForm": "tools", "offsetStart": 45, "offsetEnd": 50}, "context": "Our results underline the need for automatic tools to support annotation curation, reducing the annotation cost for domain experts.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9990249872207642}, "created": {"value": true, "score": 0.8687305450439453}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 46, "offsetEnd": 51}, "context": "There are 98,870 topic annotations for 29,616 tools with at least one topic, and 68,886 operation annotations for 28,299 tools with at least one operation.", "mentionContextAttributes": {"used": {"value": true, "score": 0.6652563214302063}, "created": {"value": false, "score": 7.271766662597656e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 47, "offsetEnd": 52}, "context": "Based on this dataset, we evaluated that 1,965 tools (6.54%) are not annotated with EDAM topic or operation, clearly showing the need for involving user communities to better annotate bioinformatics software.", "mentionContextAttributes": {"used": {"value": true, "score": 0.989544153213501}, "created": {"value": false, "score": 6.663799285888672e-05}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 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"tools", "normalizedForm": "tools", "offsetStart": 48, "offsetEnd": 53}, "context": "Basic statistics were computed on the whole bio.tools dataset, comprising 30,025 software descriptions.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9999943971633911}, "created": {"value": false, "score": 8.225440979003906e-06}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 49, "offsetEnd": 54}, "context": "Figure 2 shows the distribution of the number of tools annotated with a given number of EDAM topics or operations, considering both directly assigned annotations and inherited annotations.", "mentionContextAttributes": {"used": {"value": true, "score": 0.8626809120178223}, "created": {"value": false, "score": 1.4543533325195312e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 51, "offsetEnd": 56}, "context": "Figure 1 shows the topic annotations for these two tools, as declared in bio.tools, along with inferred annotations from the EDAM class hierarchy.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9745168685913086}, "created": {"value": false, "score": 5.793571472167969e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": 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"software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 52, "offsetEnd": 57}, "context": "This highlights the need for better curation in the tools database.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0003027915954589844}, "created": {"value": false, "score": 0.010623931884765625}, "shared": {"value": false, "score": 7.152557373046875e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 52, "offsetEnd": 57}, "context": "Finally, there are 1,114 deprecated annotations, 54 tools with at least 1 deprecated topic and 347 tools with at least 1 deprecated operation, also highlighting the need for database curation.", "mentionContextAttributes": {"used": {"value": false, "score": 0.03105682134628296}, "created": {"value": false, "score": 9.775161743164062e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 56, "offsetEnd": 60}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "Evaluating the benefits of enriched annotations and new EDAM classes requires an expert-approved gold standard.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0003426074981689453}, "created": {"value": false, "score": 0.0009034872055053711}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "bio.tools", "normalizedForm": "bio.tools", "offsetStart": 58, "offsetEnd": 67}, "context": "What is the quality of semantic annotations associated to bio.tools bioinformatics software ?", "mentionContextAttributes": {"used": {"value": false, "score": 8.237361907958984e-05}, "created": {"value": false, "score": 0.0012398958206176758}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": false, "score": 0.010901689529418945}, "created": {"value": false, "score": 0.0017705559730529785}, "shared": {"value": false, "score": 3.5762786865234375e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 62, "offsetEnd": 66}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "We also computed the number of tools annotated with redundant EDAM classes.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9999940395355225}, "created": {"value": false, "score": 5.1975250244140625e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 65, "offsetEnd": 69}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "Here we present a small example with two tools to illustrate the EDAM ontology's term hierarchy and its impact on tool search.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00018173456192016602}, "created": {"value": true, "score": 0.9994258880615234}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 65, "offsetEnd": 70}, "context": "This measure enabled us to compare the annotation quality of the tools with each other, and to identify a set of 15,929 tools (53.05%) with a low level of information annotations.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9999817609786987}, "created": {"value": false, "score": 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{"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 69, "offsetEnd": 74}, "context": "However, among the top 10 tools with the highest entropy sum, 60% of tools have redundant annotations.", "mentionContextAttributes": {"used": {"value": false, "score": 0.01235806941986084}, "created": {"value": false, "score": 2.193450927734375e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 73, "offsetEnd": 78}, "context": "We selected Qiime2 [12] and Vsearch [13] as two reference bioinformatics tools used in metagenomics data analysis.", "mentionContextAttributes": {"used": {"value": true, "score": 0.8742218613624573}, "created": {"value": false, "score": 0.00023859739303588867}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 73, "offsetEnd": 78}, "context": "Data and Format EDAM classes are not well instantiated (used) in the bio.tools registry, even though they are as important as Topic and Operation.", "mentionContextAttributes": {"used": {"value": false, "score": 0.001692056655883789}, "created": {"value": false, "score": 1.2278556823730469e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 73, "offsetEnd": 78}, "context": "The EDAM hierarchy of terms helps to enrich assigned annotations for all tools, taking ancestors into account.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00037992000579833984}, "created": {"value": false, "score": 5.14984130859375e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 77, "offsetEnd": 82}, "context": "Figure shows the topic annotations for these two tools, as declared in bio.tools, along with inferred annotations from the EDAM class hierarchy.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9503734111785889}, "created": {"value": false, "score": 6.0677528381347656e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 84, "offsetEnd": 88}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "Based on this dataset, we evaluated that 1,965 tools (6.54%) are not annotated with EDAM topic or operation, clearly showing the need for involving user communities to better annotate bioinformatics software.", "mentionContextAttributes": {"used": {"value": true, "score": 0.989544153213501}, "created": {"value": false, "score": 6.663799285888672e-05}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 88, "offsetEnd": 92}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "Figure 2 shows the distribution of the number of tools annotated with a given number of EDAM topics or operations, considering both directly assigned annotations and inherited annotations.", "mentionContextAttributes": {"used": {"value": true, "score": 0.8626809120178223}, "created": {"value": false, "score": 1.4543533325195312e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 90, "offsetEnd": 95}, "context": "We estimated that 3,405 tools (11.34%) have redundant direct topic annotations, and 2,055 tools (6.84%) have redundant direct operation annotations.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9992111921310425}, "created": {"value": false, "score": 4.649162292480469e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 93, "offsetEnd": 97}, "version": {"rawForm": "1.25", "normalizedForm": "1.25"}, "context": "We are currently working on implementing more suited metrics to better assess the quality of EDAM annotations.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00022453069686889648}, "created": {"value": true, "score": 0.9997531771659851}, "shared": {"value": false, "score": 4.76837158203125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9998369216918945}, "shared": {"value": false, "score": 8.344650268554688e-07}}, "references": [{"label": "[9]", "normalizedForm": "[9]", "refKey": 10}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 93, "offsetEnd": 98}, "context": "It is defined as the number of tools annotated by a divided by the total number of annotated tools.", "mentionContextAttributes": {"used": {"value": false, "score": 0.02680104970932007}, "created": {"value": false, "score": 6.0677528381347656e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 99, "offsetEnd": 104}, "context": "Finally, there are 1,114 deprecated annotations, 54 tools with at least 1 deprecated topic and 347 tools with at least 1 deprecated operation, also highlighting the need for database curation.", "mentionContextAttributes": {"used": {"value": false, "score": 0.03105682134628296}, "created": {"value": false, "score": 9.775161743164062e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 100, "offsetEnd": 105}, "context": "Our study focuses on the quantitative and qualitative evaluation of semantic annotations in the bio.tools registry, which serves more than 30,000 bioinformatics tool descriptions, annotated with the EDAM ontology.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0009353756904602051}, "created": {"value": true, "score": 0.6431529521942139}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 100, "offsetEnd": 105}, "context": "A low entropy for a tool indicates either that the annotations is general, or that is annotates few tools.", "mentionContextAttributes": {"used": {"value": false, "score": 0.002549588680267334}, "created": {"value": false, "score": 2.5391578674316406e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 101, "offsetEnd": 106}, "context": "Unfortunately, fewer tools are annotated by elements from these branches (among the 30 025 annotated tools 98.64 % Topics, 94.25 % Operations, 9.64 % Formats, 12.95 % Datas).", "mentionContextAttributes": {"used": {"value": false, "score": 0.10308122634887695}, "created": {"value": false, "score": 7.3909759521484375e-06}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Vsearch", "normalizedForm": "Vsearch", "offsetStart": 103, "offsetEnd": 110}, "context": "Qiime2 is annotated with topics {Microbial ecology, Phylogeny, Metatranscriptomics, Metagenomics}, and Vsearch with topics {Metagenomics, Sequence anal-ysis}.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0011646151542663574}, "created": {"value": false, "score": 6.16312026977539e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.7124571800231934}, "created": {"value": false, "score": 0.04206216335296631}, "shared": {"value": false, "score": 2.384185791015625e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 106, "offsetEnd": 111}, "context": "The more limited usage of the Format and Data branches suggest that even if they have a smaller impact on tools annotation, the margin for improvement is also higher than for Topic or", "mentionContextAttributes": {"used": {"value": false, "score": 0.0024773478507995605}, "created": {"value": false, "score": 3.6597251892089844e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 109, "offsetEnd": 114}, "context": "The distribution of tools with redundant annotations is similar in each group, with 2,369 (14.87%) redundant tools in the low information level, 2,193 (16.70%) in the medium level and 86 (8.92%) in the high level.", "mentionContextAttributes": {"used": {"value": false, "score": 0.04503864049911499}, "created": {"value": false, "score": 4.220008850097656e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, 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"offsetStart": 120, "offsetEnd": 125}, "context": "This measure enabled us to compare the annotation quality of the tools with each other, and to identify a set of 15,929 tools (53.05%) with a low level of information annotations.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9999817609786987}, "created": {"value": false, "score": 7.30752944946289e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999969005584717}, "created": {"value": true, "score": 0.9996769428253174}, "shared": {"value": false, "score": 8.344650268554688e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 121, "offsetEnd": 126}, "context": "There are 98,870 topic annotations for 29,616 tools with at least one topic, and 68,886 operation annotations for 28,299 tools with at least one operation.", "mentionContextAttributes": 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