File size: 48,148 Bytes
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"status": "PASS",
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{
"mutation": "missing_required_field",
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"reason": "'domain' is a required property\n\nFailed validating 'required' in schema:\n {'$schema': 'https://json-schema.org/draft/2020-12/schema',\n 'type': 'object',\n 'required': ['id',\n 'domain',\n 'language',\n 'library_or_tool',\n 'question_title',\n 'problem_text',\n 'question_html',\n 'code_blocks',\n 'error_text_if_explicit',\n 'attempted_method_if_explicit',\n 'answers',\n 'accepted_answer',\n 'answer_scores',\n 'source_url',\n 'author_attribution',\n 'content_license',\n 'provenance',\n 'selection_rule',\n 'group_id',\n 'split'],\n 'additionalProperties': False,\n 'properties': {'id': {'type': ['string'], 'minLength': 10},\n 'domain': {'type': ['string']},\n 'language': {'type': ['array', 'null']},\n 'library_or_tool': {'type': ['array', 'null']},\n 'question_title': {'type': ['string']},\n 'problem_text': {'type': ['string']},\n 'question_html': {'type': ['string']},\n 'code_blocks': {'type': ['array']},\n 'error_text_if_explicit': {'type': ['array', 'null']},\n 'attempted_method_if_explicit': {'type': ['null',\n 'string']},\n 'answers': {'type': ['array']},\n 'accepted_answer': {'type': ['null', 'object']},\n 'answer_scores': {'type': ['array']},\n 'source_url': {'type': ['string']},\n 'author_attribution': {'type': ['object']},\n 'content_license': {'type': ['string']},\n 'provenance': {'type': ['object'],\n 'required': ['source_dataset',\n 'source_record_id',\n 'source_record_sha256',\n 'source_license',\n 'transformation'],\n 'properties': {'source_record_sha256': {'type': 'string',\n 'pattern': '^[a-f0-9]{64}$'}}},\n 'selection_rule': {'type': ['string']},\n 'group_id': {'type': ['string'],\n 'pattern': '^[a-f0-9]{64}$'},\n 'split': {'enum': ['train',\n 'validation',\n 'test',\n 'holdout'],\n 'type': ['string']}}}\n\nOn instance:\n {'accepted_answer': None,\n 'answer_scores': [{'answer_id': 112804, 'score': 5}],\n 'answers': [{'answer_html': '<p>I know nothing about drug databases, '\n 'but am familiar with Kegg. As far as I '\n 'can see from the paper (and I may be '\n 'wrong) The drug target database would '\n 'contain the names of enzymes, the '\n 'activity of which is affected by drugs. '\n 'So the problem would seem to be to '\n 'identify so-called Kegg \u2018pathways\u2019 in '\n 'which these target enzymes occur.</p>\\n'\n '<p>(I use the adjective \u201cso-called\u201d as '\n 'Kegg pathways are not generally what a '\n 'biochemist would regard as a pathway, '\n 'but areas of metabolism. However this '\n 'would not matter if all one is trying to '\n 'do is find a correlation.)</p>\\n'\n '<p>The poster would seem, therefore, to '\n 'need to download a list of enzymes for '\n 'each Kegg pathway. At one time all the '\n 'Kegg information was available free of '\n 'charge (I downloaded a considerable '\n 'amount \u2014 although not the enzymes \u2014 to '\n 'construct a relational database). '\n 'However now one needs to purchase a '\n 'license to do this \u2014 presumably what the '\n 'authors of the paper did \u2014 at a cost of '\n 'over $1000 pa.</p>\\n'\n '<p>Unless one has grant funding or is '\n 'independently wealthy, it would seem to '\n 'be necessary to explore alternatives, '\n 'such as MetaCyc (<a '\n 'href=\"https://metacyc.org\" rel=\"nofollow '\n 'noreferrer\">https://metacyc.org</a>).</p>\\n'\n '<p><strong>Postscript</strong>\\n'\n 'The addendum from the poster shows the '\n 'UniProt IDs for the targets of the drug. '\n 'These can be converted to Kegg IDs using '\n 'the conversion tool on the Kegg site (<a '\n 'href=\"https://www.genome.jp/kegg/tool/conv_id.html\" '\n 'rel=\"nofollow '\n 'noreferrer\">https://www.genome.jp/kegg/tool/conv_id.html</a>). '\n 'The XML tag entitled \u201cpathway\u201d is not '\n 'equivalent to a Kegg metabolic pathway '\n 'as such, although the example seems to '\n 'consist of proteins involved in blood '\n 'clotting. If my interpretation is '\n 'correct, it would be irrelevant to the '\n 'procedure I suggest. However the '\n 'original paper is sufficiently vague '\n 'that I cannot be sure.</p>\\n',\n 'answer_id': 112804,\n 'answer_text': 'I know nothing about drug databases, but '\n 'am familiar with Kegg. As far as I can '\n 'see from the paper (and I may be wrong) '\n 'The drug target database would contain '\n 'the names of enzymes, the activity of '\n 'which is affected by drugs. So the '\n 'problem would seem to be to identify '\n 'so-called Kegg \u2018pathways\u2019 in which these '\n 'target enzymes occur.\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n '(I use the adjective \u201cso-called\u201d as Kegg '\n 'pathways are not generally what a '\n 'biochemist would regard as a pathway, '\n 'but areas of metabolism. However this '\n 'would not matter if all one is trying to '\n 'do is find a correlation.)\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n 'The poster would seem, therefore, to '\n 'need to download a list of enzymes for '\n 'each Kegg pathway. At one time all the '\n 'Kegg information was available free of '\n 'charge (I downloaded a considerable '\n 'amount \u2014 although not the enzymes \u2014 to '\n 'construct a relational database). '\n 'However now one needs to purchase a '\n 'license to do this \u2014 presumably what the '\n 'authors of the paper did \u2014 at a cost of '\n 'over $1000 pa.\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n 'Unless one has grant funding or is '\n 'independently wealthy, it would seem to '\n 'be necessary to explore alternatives, '\n 'such as MetaCyc (https://metacyc.org '\n '(https://metacyc.org)).\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n 'Postscript\\n'\n 'The addendum from the poster shows the '\n 'UniProt IDs for the targets of the drug. '\n 'These can be converted to Kegg IDs using '\n 'the conversion tool on the Kegg site '\n '(https://www.genome.jp/kegg/tool/conv_id.html '\n '(https://www.genome.jp/kegg/tool/conv_id.html)). '\n 'The XML tag entitled \u201cpathway\u201d is not '\n 'equivalent to a Kegg metabolic pathway '\n 'as such, although the example seems to '\n 'consist of proteins involved in blood '\n 'clotting. If my interpretation is '\n 'correct, it would be irrelevant to the '\n 'procedure I suggest. However the '\n 'original paper is sufficiently vague '\n 'that I cannot be sure.',\n 'answer_url': 'https://biology.stackexchange.com/a/112804',\n 'author': 'David',\n 'author_url': 'https://biology.stackexchange.com/users/22057/david',\n 'content_license': 'CC BY-SA 4.0',\n 'created_at': '2023-08-13T11:37:13+00:00',\n 'is_accepted': False,\n 'provenance': {'attribution_required': True,\n 'collected_at': '2026-10-01T03:03:38.885561+00:00',\n 'license': 'CC BY-SA 4.0',\n 'license_url': 'https://creativecommons.org/licenses/by-sa/4.0/',\n 'raw_file': 'raw/codex_api_v1/a145de97eabc007745b45919875489a41261075cbdf33d916d9640ba4ad0bd35_0.json',\n 'raw_sha256': 'e7d8d4315eef8e039a452d2811869cbe305575c6ff8a6bef8f80d6dfb58c5bfd',\n 'source_api': 'Stack Exchange API 2.3',\n 'source_url': 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'revision_url': 'https://biology.stackexchange.com/revisions/2D4BC5F7-1B1B-44D3-BB31-EB109B8535CB/view-source'}],\n 'score': 5}],\n 'attempted_method_if_explicit': None,\n 'author_attribution': {'answers': [{'author': 'David',\n 'author_url': 'https://biology.stackexchange.com/users/22057/david',\n 'content_license': 'CC BY-SA 4.0',\n 'revision_attribution': [{'content_license': 'CC '\n 'BY-SA '\n '4.0',\n 'contributor': {'display_name': 'David',\n 'profile_url': 'https://biology.stackexchange.com/users/22057/david',\n 'user_type': 'registered'},\n 'created_at': '2023-08-13T11:37:13+00:00',\n 'raw_file': 'raw/codex_api_v1/9b8fea4e5df4051aa25c1aa90b42eca7481ee703f92ba25aeabed3d0b53e7a04_1790824026598483100_0.json',\n 'raw_sha256': 'f252fc1b154815b8794116efb3b685202eda8dddb2cd870ae32ee5e82716c300',\n 'revision_guid': '2D881A87-9785-460D-8B6A-4D609910C727',\n 'revision_number': 1,\n 'revision_type': 'single_user',\n 'revision_url': 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<drug>\\n'\n ' '\n '<drugbank-id>DB01022</drugbank-id>\\n'\n ' <name>Phylloquinone</name>\\n'\n ' </drug>\\n'\n ' <drug>\\n'\n ' '\n '<drugbank-id>DB01373</drugbank-id>\\n'\n ' <name>Calcium</name>\\n'\n ' </drug>\\n'\n ' </drugs>\\n'\n ' <enzymes>\\n'\n ' '\n '<uniprot-id>P00734</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00748</uniprot-id>\\n'\n ' '\n '<uniprot-id>P02452</uniprot-id>\\n'\n ' '\n '<uniprot-id>P03952</uniprot-id>\\n'\n ' '\n '<uniprot-id>P03951</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00740</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00451</uniprot-id>\\n'\n ' '\n '<uniprot-id>P12259</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00742</uniprot-id>\\n'\n ' '\n '<uniprot-id>P02671</uniprot-id>\\n'\n ' '\n '<uniprot-id>P02675</uniprot-id>\\n'\n ' '\n '<uniprot-id>P02679</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00488</uniprot-id>\\n'\n ' '\n '<uniprot-id>P05160</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00747</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00750</uniprot-id>\\n'\n ' '\n '<uniprot-id>P08709</uniprot-id>\\n'\n ' '\n '<uniprot-id>P13726</uniprot-id>\\n'\n ' '\n '<uniprot-id>Q9BQB6</uniprot-id>\\n'\n ' '\n '<uniprot-id>P38435</uniprot-id>\\n'\n ' </enzymes>\\n'\n ' </pathway>\\n'\n ' </pathways>\\n'\n '\\n'\n '```\\n',\n 'post_id': '112789',\n 'sha256': '4452dea3b66a2c29df5a54e5e802e54d6339b7f0a59f86f15142323a44138d31',\n 'source_url': 'https://biology.stackexchange.com/questions/112789/how-to-generate-pathway-fingerprints-of-drugs'}],\n 'content_license': 'CC BY-SA 4.0',\n 'error_text_if_explicit': None,\n 'group_id': '21341a8f8da58f78f0df843bca6c30524caaad2ffd24c0988a87895e0f6d2c2c',\n 'id': 'SCT-888cccfd7708642b5b451223',\n 'language': None,\n 'library_or_tool': None,\n 'problem_text': 'I have studied a paper that constructs the pathway '\n 'fingerprint of a drug, which has a vector of $0$ and '\n '$1$, and they compare the pathway fingerprint using '\n 'a similarity measure to assess how similar the drugs '\n 'are.\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n \"But I don't know where can I download pathways and \"\n 'how to generate their fingerprint vector to evaluate '\n 'them. I checked KEGG website '\n '(https://www.genome.jp/kegg/) but could not find '\n 'anything there to download. The paper can be '\n 'downloaded from: '\n 'https://pubmed.ncbi.nlm.nih.gov/22426982/ '\n '(https://pubmed.ncbi.nlm.nih.gov/22426982/)\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n 'I really appreciate answers that can help me to '\n 'solve the problem.\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n 'Update\\n'\n 'Since i am not familiar with DrugBank and biology '\n 'science, when I parsed the xml file of drugbank, I '\n 'find a tag with name pathway . But i am not sure '\n 'that do these elements show the pathway of drug or '\n 'not? Is it possible to use them to construct the '\n 'pathway fingerprint vector for drugs? what does '\n '<uniprot-id>P00734</uniprot-id> mean?\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n 'this is the content of pathway tag for Lepirudin:\\n'\n '\\n'\n '\\n'\n '\\n'\n '\\n'\n '<pathways>\\n'\n ' <pathway>\\n'\n ' <smpdb-id>SMP0000278</smpdb-id>\\n'\n ' <name>Lepirudin Action Pathway</name>\\n'\n ' <category>drug_action</category>\\n'\n ' <drugs>\\n'\n ' <drug>\\n'\n ' <drugbank-id>DB00001</drugbank-id>\\n'\n ' <name>Lepirudin</name>\\n'\n ' </drug>\\n'\n ' <drug>\\n'\n ' <drugbank-id>DB01022</drugbank-id>\\n'\n ' <name>Phylloquinone</name>\\n'\n ' </drug>\\n'\n ' <drug>\\n'\n ' <drugbank-id>DB01373</drugbank-id>\\n'\n ' <name>Calcium</name>\\n'\n ' </drug>\\n'\n ' </drugs>\\n'\n ' <enzymes>\\n'\n ' <uniprot-id>P00734</uniprot-id>\\n'\n ' <uniprot-id>P00748</uniprot-id>\\n'\n ' <uniprot-id>P02452</uniprot-id>\\n'\n ' <uniprot-id>P03952</uniprot-id>\\n'\n ' <uniprot-id>P03951</uniprot-id>\\n'\n ' <uniprot-id>P00740</uniprot-id>\\n'\n ' <uniprot-id>P00451</uniprot-id>\\n'\n ' <uniprot-id>P12259</uniprot-id>\\n'\n ' <uniprot-id>P00742</uniprot-id>\\n'\n ' <uniprot-id>P02671</uniprot-id>\\n'\n ' <uniprot-id>P02675</uniprot-id>\\n'\n ' <uniprot-id>P02679</uniprot-id>\\n'\n ' <uniprot-id>P00488</uniprot-id>\\n'\n ' <uniprot-id>P05160</uniprot-id>\\n'\n ' <uniprot-id>P00747</uniprot-id>\\n'\n ' <uniprot-id>P00750</uniprot-id>\\n'\n ' <uniprot-id>P08709</uniprot-id>\\n'\n ' <uniprot-id>P13726</uniprot-id>\\n'\n ' <uniprot-id>Q9BQB6</uniprot-id>\\n'\n ' <uniprot-id>P38435</uniprot-id>\\n'\n ' </enzymes>\\n'\n ' </pathway>\\n'\n ' </pathways>\\n'\n '\\n'\n '```',\n 'provenance': {'original_provenance': {'attribution_required': True,\n 'collected_at': '2026-10-01T03:03:12.794960+00:00',\n 'license': 'CC BY-SA 4.0',\n 'license_url': 'https://creativecommons.org/licenses/by-sa/4.0/',\n 'raw_file': 'raw/codex_api_v1/01e5186067e30dc1b8d7a145670ab7edd6b017797b271a481af8b7b7f55f13c2_0.json',\n 'raw_sha256': '6c3960de7e1d3d7920bb88d02e2184614c219b391f39d9bddc2a582fdc9a71e7',\n 'source_api': 'Stack Exchange '\n 'API 2.3',\n 'source_url': 'https://api.stackexchange.com/2.3/search/advanced?answers=1&filter=withbody&order=desc&page=10&pagesize=100&site=biology&sort=creation',\n 'transformation': 'API HTML '\n 'retained; 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no LLM truth '\n 'labels'},\n 'question_html': '<p>I have studied a paper that constructs the '\n 'pathway fingerprint of a drug, which has a vector '\n 'of <span class=\"math-container\">$0$</span> and '\n '<span class=\"math-container\">$1$</span>, and they '\n 'compare the pathway fingerprint using a similarity '\n 'measure to assess how similar the drugs are.</p>\\n'\n \"<p>But I don't know where can I download pathways \"\n 'and how to generate their fingerprint vector to '\n 'evaluate them. I checked <a '\n 'href=\"https://www.genome.jp/kegg/\" rel=\"nofollow '\n 'noreferrer\">KEGG website</a> but could not find '\n 'anything there to download. The paper can be '\n 'downloaded from: <a '\n 'href=\"https://pubmed.ncbi.nlm.nih.gov/22426982/\" '\n 'rel=\"nofollow '\n 'noreferrer\">https://pubmed.ncbi.nlm.nih.gov/22426982/</a></p>\\n'\n '<p>I really appreciate answers that can help me to '\n 'solve the problem.</p>\\n'\n '<p><strong>Update</strong>\\n'\n 'Since i am not familiar with DrugBank and biology '\n 'science, when I parsed the xml file of drugbank, I '\n 'find a tag with name <code>pathway</code> . But i '\n 'am not sure that do these elements show the pathway '\n 'of drug or not? Is it possible to use them to '\n 'construct the pathway fingerprint vector for drugs? '\n 'what does '\n '<code><uniprot-id>P00734</uniprot-id></code> '\n 'mean?</p>\\n'\n '<p>this is the content of <code>pathway</code> tag '\n 'for Lepirudin:</p>\\n'\n '<pre><code><pathways>\\n'\n ' <pathway>\\n'\n ' <smpdb-id>SMP0000278</smpdb-id>\\n'\n ' <name>Lepirudin Action '\n 'Pathway</name>\\n'\n ' <category>drug_action</category>\\n'\n ' <drugs>\\n'\n ' <drug>\\n'\n ' '\n '<drugbank-id>DB00001</drugbank-id>\\n'\n ' <name>Lepirudin</name>\\n'\n ' </drug>\\n'\n ' <drug>\\n'\n ' '\n '<drugbank-id>DB01022</drugbank-id>\\n'\n ' <name>Phylloquinone</name>\\n'\n ' </drug>\\n'\n ' <drug>\\n'\n ' '\n '<drugbank-id>DB01373</drugbank-id>\\n'\n ' <name>Calcium</name>\\n'\n ' </drug>\\n'\n ' </drugs>\\n'\n ' <enzymes>\\n'\n ' '\n '<uniprot-id>P00734</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00748</uniprot-id>\\n'\n ' '\n '<uniprot-id>P02452</uniprot-id>\\n'\n ' '\n '<uniprot-id>P03952</uniprot-id>\\n'\n ' '\n '<uniprot-id>P03951</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00740</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00451</uniprot-id>\\n'\n ' '\n '<uniprot-id>P12259</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00742</uniprot-id>\\n'\n ' '\n '<uniprot-id>P02671</uniprot-id>\\n'\n ' '\n '<uniprot-id>P02675</uniprot-id>\\n'\n ' '\n '<uniprot-id>P02679</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00488</uniprot-id>\\n'\n ' '\n '<uniprot-id>P05160</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00747</uniprot-id>\\n'\n ' '\n '<uniprot-id>P00750</uniprot-id>\\n'\n ' '\n '<uniprot-id>P08709</uniprot-id>\\n'\n ' '\n '<uniprot-id>P13726</uniprot-id>\\n'\n ' '\n '<uniprot-id>Q9BQB6</uniprot-id>\\n'\n ' '\n '<uniprot-id>P38435</uniprot-id>\\n'\n ' </enzymes>\\n'\n ' </pathway>\\n'\n ' </pathways>\\n'\n '\\n'\n '<span class=\"math-container\">```</span>\\n'\n '</code></pre>\\n',\n 'question_title': 'How to generate pathway fingerprints of drugs?',\n 'selection_rule': 'question troubleshooting lexeme plus literal pre '\n 'block in question or answer; no root-cause '\n 'inference',\n 'source_url': 'https://biology.stackexchange.com/questions/112789/how-to-generate-pathway-fingerprints-of-drugs',\n 'split': 'holdout'}"
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