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Merge pull request #8 from ai4curation/batch5
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‎.claude/hooks/protect_files_hook.py‎

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PROTECTED_PATH_FRAGMENTS = [
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"publications",
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"deep-research.md",
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"ai-review.md",
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"goa.tsv",
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".uniprot.txt",
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]

‎app/data.js‎

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‎assets/docs/ActionEnum.md‎

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| MARK_AS_OVER_ANNOTATED | The term is not entirely wrong, but likely represents an over-annotation of the gene | | |
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| UNDECIDED | The annotation is not clear, and the reviewer is not sure what to do with it. ALWAYS USE THIS IF YOU ARE UNABLE TO ACCESS RELEVANT PUBLICATIONS | | |
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| PENDING | The review entry is a stub, and the review has not been completed yet. | | |
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| NEW | This is a proposed annotation, not one that exists in the existing GO annotations. Use this to propose a new annotation not covered by the existing GO annotations. Use this conservatively, do not over-annotate, especially for biological process. Do not use for indirect or pleiotropic effects. Be sure you have good evidence, this can be from multiple sources. | | |

‎assets/docs/EvidenceType.md‎

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# Enum: EvidenceType
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Gene Ontology evidence codes mapped to Evidence and Conclusion Ontology (ECO) terms
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URI: [gene_review:EvidenceType](https://w3id.org/ai4curation/gene_review/EvidenceType)
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| Text | Description | Meaning | Other Information |
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| :--- | :---: | :---: | ---: |
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| IDA | | | |
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| IBA | | | |
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| ISS | | | |
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| TAS | | | |
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| IEP | | | |
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| IGC | | | |
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| EXP | Inferred from Experiment | ECO:0000269 | |
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| IDA | Inferred from Direct Assay | ECO:0000314 | |
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| IPI | Inferred from Physical Interaction | ECO:0000353 | |
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| IMP | Inferred from Mutant Phenotype | ECO:0000315 | |
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| IGI | Inferred from Genetic Interaction | ECO:0000316 | |
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| IEP | Inferred from Expression Pattern | ECO:0000270 | |
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| HTP | Inferred from High Throughput Experiment | ECO:0006056 | |
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| HDA | Inferred from High Throughput Direct Assay | ECO:0007005 | |
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| HMP | Inferred from High Throughput Mutant Phenotype | ECO:0007001 | |
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| HGI | Inferred from High Throughput Genetic Interaction | ECO:0007003 | |
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| HEP | Inferred from High Throughput Expression Pattern | ECO:0007007 | |
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| IBA | Inferred from Biological aspect of Ancestor | ECO:0000318 | |
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| IBD | Inferred from Biological aspect of Descendant | ECO:0000319 | |
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| IKR | Inferred from Key Residues | ECO:0000320 | |
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| IRD | Inferred from Rapid Divergence | ECO:0000321 | |
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| ISS | Inferred from Sequence or structural Similarity | ECO:0000250 | |
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| ISO | Inferred from Sequence Orthology | ECO:0000266 | |
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| ISA | Inferred from Sequence Alignment | ECO:0000247 | |
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| ISM | Inferred from Sequence Model | ECO:0000255 | |
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| IGC | Inferred from Genomic Context | ECO:0000317 | |
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| RCA | Inferred from Reviewed Computational Analysis | ECO:0000245 | |
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| TAS | Traceable Author Statement | ECO:0000304 | |
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| NAS | Non-traceable Author Statement | ECO:0000303 | |
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| IC | Inferred by Curator | ECO:0000305 | |
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| ND | No biological Data available | ECO:0000307 | |
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| IEA | Inferred from Electronic Annotation | ECO:0000501 | |

‎assets/docs/ExistingAnnotation.md‎

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URI: [gene_review:ExistingAnnotation](https://w3id.org/ai4curation/gene_review/ExistingAnnotation)
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Term],[Review],[Reference],[Review]<review%200..1-++[ExistingAnnotation&#124;negated:boolean%20%3F;evidence_type:string%20%3F;supporting_entities:string%20*],[Reference]<original_reference_id%200..1-%20[ExistingAnnotation],[AnnotationExtension]<extensions%200..*-++[ExistingAnnotation],[Term]<term%200..1-++[ExistingAnnotation],[GeneReview]++-%20existing_annotations%200..*>[ExistingAnnotation],[GeneReview],[AnnotationExtension])](https://yuml.me/diagram/nofunky;dir:TB/class/[Term],[Review],[Reference],[Review]<review%200..1-++[ExistingAnnotation&#124;negated:boolean%20%3F;evidence_type:string%20%3F;supporting_entities:string%20*],[Reference]<original_reference_id%200..1-%20[ExistingAnnotation],[AnnotationExtension]<extensions%200..*-++[ExistingAnnotation],[Term]<term%200..1-++[ExistingAnnotation],[GeneReview]++-%20existing_annotations%200..*>[ExistingAnnotation],[GeneReview],[AnnotationExtension])
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Term],[Review],[Reference],[Review]<review%200..1-++[ExistingAnnotation&#124;negated:boolean%20%3F;evidence_type:EvidenceType%20%3F;supporting_entities:string%20*],[Reference]<original_reference_id%200..1-%20[ExistingAnnotation],[AnnotationExtension]<extensions%200..*-++[ExistingAnnotation],[Term]<term%200..1-++[ExistingAnnotation],[GeneReview]++-%20existing_annotations%200..*>[ExistingAnnotation],[GeneReview],[AnnotationExtension])](https://yuml.me/diagram/nofunky;dir:TB/class/[Term],[Review],[Reference],[Review]<review%200..1-++[ExistingAnnotation&#124;negated:boolean%20%3F;evidence_type:EvidenceType%20%3F;supporting_entities:string%20*],[Reference]<original_reference_id%200..1-%20[ExistingAnnotation],[AnnotationExtension]<extensions%200..*-++[ExistingAnnotation],[Term]<term%200..1-++[ExistingAnnotation],[GeneReview]++-%20existing_annotations%200..*>[ExistingAnnotation],[GeneReview],[AnnotationExtension])
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## Referenced by Class
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* Range: [Boolean](types/Boolean.md)
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* [evidence_type](evidence_type.md) <sub>0..1</sub>
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* Description: Evidence code (e.g., IDA, IBA, ISS, TAS)
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* Range: [String](types/String.md)
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* Range: [EvidenceType](EvidenceType.md)
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* [original_reference_id](original_reference_id.md) <sub>0..1</sub>
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* Description: ID of the original reference
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* Range: [Reference](Reference.md)

‎assets/docs/Finding.md‎

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URI: [gene_review:Finding](https://w3id.org/ai4curation/gene_review/Finding)
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reference]++-%20findings%200..*>[Finding&#124;statement:string%20%3F;supporting_text:string%20%3F;reference_section_type:string%20%3F],[Reference])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reference]++-%20findings%200..*>[Finding&#124;statement:string%20%3F;supporting_text:string%20%3F;reference_section_type:string%20%3F],[Reference])
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reference]++-%20findings%200..*>[Finding&#124;statement:string%20%3F;supporting_text:string%20%3F;full_text_unavailable:boolean%20%3F;reference_section_type:ManuscriptSection%20%3F],[Reference])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reference]++-%20findings%200..*>[Finding&#124;statement:string%20%3F;supporting_text:string%20%3F;full_text_unavailable:boolean%20%3F;reference_section_type:ManuscriptSection%20%3F],[Reference])
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## Referenced by Class
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* [supporting_text](supporting_text.md) <sub>0..1</sub>
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* Description: Supporting text from the publication. This should be exact substrings. Different substrings can be broken up by '...'s. These substrings will be checked against the actual text of the paper. If editorialization is necessary, put this in square brackets (this is not checked). For example, you can say '...[CFAP300 shows] transport within cilia is IFT dependent...'
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* Range: [String](types/String.md)
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* [full_text_unavailable](full_text_unavailable.md) <sub>0..1</sub>
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* Description: Whether the full text is unavailable
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* Range: [Boolean](types/Boolean.md)
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* [reference_section_type](reference_section_type.md) <sub>0..1</sub>
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* Description: Type of section in the reference (e.g., 'ABSTRACT', 'METHODS', 'RESULTS', 'DISCUSSION')
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* Range: [String](types/String.md)
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* Range: [ManuscriptSection](ManuscriptSection.md)

‎assets/docs/ProposedOntologyTerm.md‎

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URI: [gene_review:ProposedOntologyTerm](https://w3id.org/ai4curation/gene_review/ProposedOntologyTerm)
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneReview]++-%20proposed_new_terms%200..*>[ProposedOntologyTerm&#124;proposed_name:string;proposed_definition:string;justification:string%20%3F],[GeneReview])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneReview]++-%20proposed_new_terms%200..*>[ProposedOntologyTerm&#124;proposed_name:string;proposed_definition:string;justification:string%20%3F],[GeneReview])
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[SupportingTextInReference],[SupportingTextInReference]<supported_by%200..*-++[ProposedOntologyTerm&#124;proposed_name:string;proposed_definition:string;justification:string%20%3F],[GeneReview]++-%20proposed_new_terms%200..*>[ProposedOntologyTerm],[GeneReview])](https://yuml.me/diagram/nofunky;dir:TB/class/[SupportingTextInReference],[SupportingTextInReference]<supported_by%200..*-++[ProposedOntologyTerm&#124;proposed_name:string;proposed_definition:string;justification:string%20%3F],[GeneReview]++-%20proposed_new_terms%200..*>[ProposedOntologyTerm],[GeneReview])
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## Referenced by Class
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* [➞justification](proposedOntologyTerm__justification.md) <sub>0..1</sub>
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* Description: Justification for why this term is needed
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* Range: [String](types/String.md)
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* [➞supported_by](proposedOntologyTerm__supported_by.md) <sub>0..\*</sub>
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* Range: [SupportingTextInReference](SupportingTextInReference.md)

‎assets/docs/Reference.md‎

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URI: [gene_review:Reference](https://w3id.org/ai4curation/gene_review/Reference)
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Finding]<findings%200..*-++[Reference&#124;id:string;title:string;is_invalid:boolean%20%3F],[Review]-%20additional_reference_ids%200..*>[Reference],[ExistingAnnotation]-%20original_reference_id%200..1>[Reference],[SupportingTextInReference]-%20reference_id%200..1>[Reference],[GeneReview]++-%20references%200..*>[Reference],[SupportingTextInReference],[Review],[GeneReview],[Finding],[ExistingAnnotation])](https://yuml.me/diagram/nofunky;dir:TB/class/[Finding]<findings%200..*-++[Reference&#124;id:string;title:string;is_invalid:boolean%20%3F],[Review]-%20additional_reference_ids%200..*>[Reference],[ExistingAnnotation]-%20original_reference_id%200..1>[Reference],[SupportingTextInReference]-%20reference_id%200..1>[Reference],[GeneReview]++-%20references%200..*>[Reference],[SupportingTextInReference],[Review],[GeneReview],[Finding],[ExistingAnnotation])
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Finding]<findings%200..*-++[Reference&#124;id:string;title:string;is_invalid:boolean%20%3F;full_text_unavailable:boolean%20%3F],[Review]-%20additional_reference_ids%200..*>[Reference],[ExistingAnnotation]-%20original_reference_id%200..1>[Reference],[SupportingTextInReference]-%20reference_id%200..1>[Reference],[GeneReview]++-%20references%200..*>[Reference],[SupportingTextInReference],[Review],[GeneReview],[Finding],[ExistingAnnotation])](https://yuml.me/diagram/nofunky;dir:TB/class/[Finding]<findings%200..*-++[Reference&#124;id:string;title:string;is_invalid:boolean%20%3F;full_text_unavailable:boolean%20%3F],[Review]-%20additional_reference_ids%200..*>[Reference],[ExistingAnnotation]-%20original_reference_id%200..1>[Reference],[SupportingTextInReference]-%20reference_id%200..1>[Reference],[GeneReview]++-%20references%200..*>[Reference],[SupportingTextInReference],[Review],[GeneReview],[Finding],[ExistingAnnotation])
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## Referenced by Class
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* [is_invalid](is_invalid.md) <sub>0..1</sub>
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* Description: Whether the reference is invalid (e.g., retracted or replaced)
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* Range: [Boolean](types/Boolean.md)
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* [full_text_unavailable](full_text_unavailable.md) <sub>0..1</sub>
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* Description: Whether the full text is unavailable
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* Range: [Boolean](types/Boolean.md)

‎assets/docs/SupportingTextInReference.md‎

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URI: [gene_review:SupportingTextInReference](https://w3id.org/ai4curation/gene_review/SupportingTextInReference)
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reference]<reference_id%200..1-%20[SupportingTextInReference&#124;supporting_text:string%20%3F;reference_section_type:string%20%3F],[CoreFunction]++-%20supported_by%200..*>[SupportingTextInReference],[Review]++-%20supported_by%200..*>[SupportingTextInReference],[Review],[Reference],[CoreFunction])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reference]<reference_id%200..1-%20[SupportingTextInReference&#124;supporting_text:string%20%3F;reference_section_type:string%20%3F],[CoreFunction]++-%20supported_by%200..*>[SupportingTextInReference],[Review]++-%20supported_by%200..*>[SupportingTextInReference],[Review],[Reference],[CoreFunction])
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[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reference]<reference_id%200..1-%20[SupportingTextInReference&#124;supporting_text:string%20%3F;full_text_unavailable:boolean%20%3F;reference_section_type:ManuscriptSection%20%3F],[CoreFunction]++-%20supported_by%200..*>[SupportingTextInReference],[ProposedOntologyTerm]++-%20supported_by%200..*>[SupportingTextInReference],[Review]++-%20supported_by%200..*>[SupportingTextInReference],[Review],[Reference],[ProposedOntologyTerm],[CoreFunction])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reference]<reference_id%200..1-%20[SupportingTextInReference&#124;supporting_text:string%20%3F;full_text_unavailable:boolean%20%3F;reference_section_type:ManuscriptSection%20%3F],[CoreFunction]++-%20supported_by%200..*>[SupportingTextInReference],[ProposedOntologyTerm]++-%20supported_by%200..*>[SupportingTextInReference],[Review]++-%20supported_by%200..*>[SupportingTextInReference],[Review],[Reference],[ProposedOntologyTerm],[CoreFunction])
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## Referenced by Class
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* **None** *[➞supported_by](coreFunction__supported_by.md)* <sub>0..\*</sub> **[SupportingTextInReference](SupportingTextInReference.md)**
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* **None** *[➞supported_by](proposedOntologyTerm__supported_by.md)* <sub>0..\*</sub> **[SupportingTextInReference](SupportingTextInReference.md)**
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* **None** *[supported_by](supported_by.md)* <sub>0..\*</sub> **[SupportingTextInReference](SupportingTextInReference.md)**
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## Attributes
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* [supporting_text](supporting_text.md) <sub>0..1</sub>
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* Description: Supporting text from the publication. This should be exact substrings. Different substrings can be broken up by '...'s. These substrings will be checked against the actual text of the paper. If editorialization is necessary, put this in square brackets (this is not checked). For example, you can say '...[CFAP300 shows] transport within cilia is IFT dependent...'
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* Range: [String](types/String.md)
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* [full_text_unavailable](full_text_unavailable.md) <sub>0..1</sub>
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* Description: Whether the full text is unavailable
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* Range: [Boolean](types/Boolean.md)
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* [reference_section_type](reference_section_type.md) <sub>0..1</sub>
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* Description: Type of section in the reference (e.g., 'ABSTRACT', 'METHODS', 'RESULTS', 'DISCUSSION')
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* Range: [String](types/String.md)
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* Range: [ManuscriptSection](ManuscriptSection.md)

‎assets/docs/evidence_type.md‎

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## Domain and Range
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None &#8594; <sub>0..1</sub> [String](types/String.md)
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None &#8594; <sub>0..1</sub> [EvidenceType](EvidenceType.md)
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## Parents
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