Index

_

__all_names() (aoptk.chemical.Chemical method) __author__ (in module aoptk.relationships) __email__ (in module aoptk.relationships) __eq__() (aoptk.chemical.Chemical method) (aoptk.effect.Effect method) (aoptk.literature.id.ID method) __eq_chemical() (aoptk.chemical.Chemical method) __eq_object() (aoptk.chemical.Chemical method) __hash__() (aoptk.chemical.Chemical method) (aoptk.effect.Effect method) (aoptk.literature.id.ID method) __str__() (aoptk.chemical.Chemical method) (aoptk.effect.Effect method) (aoptk.literature.abstract.Abstract method) (aoptk.literature.id.DOI method) (aoptk.literature.id.ID method) (aoptk.literature.id.PMCID method) (aoptk.literature.id.PMID method) (aoptk.literature.pdf.PDF method) (aoptk.literature.publication.Publication method) (aoptk.literature.publication_metadata.PublicationMetadata method) (aoptk.relationships.relationship.Relationship method) __version__ (in module aoptk) (in module aoptk.relationships) _async_get_publication_count_and_ids() (aoptk.literature.databases.pmc.PMC method) _call_api() (aoptk.literature.databases.europepmc.EuropePMC method) _classify_relationships_in_table() (aoptk.text_generation_api.TextGenerationAPI method) _classify_relationships_in_text_and_images() (aoptk.text_generation_api.TextGenerationAPI method) _clean_control_chars() (aoptk.literature.pymupdf_parser.PymupdfParser method) _collect_ids_for_year() (aoptk.literature.databases.pmc.PMC method) _collect_ids_split_by_months_days() (aoptk.literature.databases.pmc.PMC method) _database_path (aoptk.normalization.provide_mesh_term_dataframe_from_xml.ProvideMeshTermDataframeFromXML attribute) _encode_image() (aoptk.text_generation_api.TextGenerationAPI method) _extract_abstract() (aoptk.literature.pymupdf_parser.PymupdfParser method) _extract_figure_descriptions() (aoptk.literature.pymupdf_parser.PymupdfParser method) _extract_figures() (aoptk.literature.pymupdf_parser.PymupdfParser method) _extract_figures_from_supplements() (aoptk.literature.databases.pmc.PMC method) _extract_full_text() (aoptk.literature.pymupdf_parser.PymupdfParser method) _extract_full_text_from_images() (aoptk.literature.pymupdf_parser.PymupdfParser method) _extract_pdf_as_images() (aoptk.literature.pymupdf_parser.PymupdfParser method) _extract_rows() (aoptk.literature.databases.europepmc.EuropePMC method) _extract_text_blocks_without_irrelevant_border_text() (aoptk.literature.pymupdf_parser.PymupdfParser method) _extract_text_to_parse() (aoptk.literature.pymupdf_parser.PymupdfParser method) _figure_large_enough() (aoptk.literature.pymupdf_parser.PymupdfParser method) _find_matching_name() (aoptk.text_generation_api.TextGenerationAPI method)

_find_synonyms_in_pubchem() (aoptk.normalization.pubchem_api.PubChemAPI method) _find_title_in_pubchem() (aoptk.normalization.pubchem_api.PubChemAPI method) _get_abstract() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pubmed.PubMed method) _get_figures() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pmc.PMC method) _get_file() (aoptk.literature.databases.pmc.PMC method) _get_full_text() (aoptk.literature.databases.pmc.PMC method) _get_json() (aoptk.literature.databases.pmc.PMC method) _get_pdf() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pmc.PMC method) _get_publication() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pmc.PMC method) _get_publication_count_and_ids() (aoptk.literature.databases.pmc.PMC method) _get_publication_id() (in module aoptk.literature.databases.europepmc) _get_publication_metadata() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pubmed.PubMed method) _get_supplementary_zip_path() (aoptk.literature.databases.europepmc.EuropePMC method) _get_xml() (aoptk.literature.databases.europepmc.EuropePMC method) _heading (aoptk.chemical.Chemical attribute) _is_corrupted() (aoptk.literature.pymupdf_parser.PymupdfParser method) _is_too_short() (aoptk.literature.pymupdf_parser.PymupdfParser method) _lock (aoptk.literature.utils.AsyncRequestLimiter attribute) _mesh_terms (aoptk.normalization.mesh_terms.MeshTerms attribute) _name (aoptk.chemical.Chemical attribute) (aoptk.effect.Effect attribute) _next_allowed (aoptk.literature.utils.AsyncRequestLimiter attribute) _parse_pdf() (aoptk.literature.pymupdf_parser.PymupdfParser method) _parse_xml_abstract() (aoptk.literature.databases.europepmc.EuropePMC method) _parse_xml_figure_descriptions() (aoptk.literature.databases.europepmc.EuropePMC method) _parse_xml_full_text() (aoptk.literature.databases.europepmc.EuropePMC method) _parse_xml_tables() (aoptk.literature.databases.europepmc.EuropePMC method) _process_colon_separated_response() (aoptk.text_generation_api.TextGenerationAPI method) _prompt() (aoptk.text_generation_api.TextGenerationAPI method) _query (aoptk.literature.databases.europepmc.EuropePMC attribute) (aoptk.literature.databases.pmc.PMC attribute) (aoptk.literature.databases.pubmed.PubMed attribute) _relationship_prompt() (aoptk.text_generation_api.TextGenerationAPI method) _render_prompt() (aoptk.text_generation_api.TextGenerationAPI method) _save_figure() (aoptk.literature.pymupdf_parser.PymupdfParser method) _select_relationship_type() (aoptk.text_generation_api.TextGenerationAPI method) _session (aoptk.literature.databases.europepmc.EuropePMC attribute) (aoptk.normalization.pubchem_api.PubChemAPI attribute) _synonyms (aoptk.chemical.Chemical attribute) (aoptk.normalization.pubchem_local.PubChemSynonyms attribute) _write_pdf() (aoptk.literature.databases.europepmc.EuropePMC method)

A

abstract (aoptk.literature.publication.Publication attribute) Abstract (class in aoptk.literature.abstract) abstracts_only() (aoptk.literature.databases.europepmc.EuropePMC method) aoptk module aoptk.chemical module aoptk.effect module aoptk.find_chemical module aoptk.literature module aoptk.literature.abstract module aoptk.literature.convert_image module aoptk.literature.convert_pdf_scan module aoptk.literature.databases module aoptk.literature.databases.europepmc module aoptk.literature.databases.pmc module aoptk.literature.databases.pubmed module aoptk.literature.find_relevant_publication module aoptk.literature.get_abstract module aoptk.literature.get_id module aoptk.literature.get_pdf module aoptk.literature.get_publication module aoptk.literature.get_publication_metadata module aoptk.literature.id module

aoptk.literature.pdf module aoptk.literature.pdf_parser module aoptk.literature.publication module aoptk.literature.publication_metadata module aoptk.literature.pymupdf_parser module aoptk.literature.utils module aoptk.normalization module aoptk.normalization.mesh_terms module aoptk.normalization.normalize_chemical module aoptk.normalization.provide_mesh_term_dataframe_from_xml module aoptk.normalization.provide_normalization_dataframe module aoptk.normalization.pubchem_api module aoptk.normalization.pubchem_local module aoptk.relationship_type module aoptk.relationships module aoptk.relationships.find_relationship module aoptk.relationships.relationship module aoptk.text_generation_api module aoptk.text_utils module api_key (aoptk.text_generation_api.TextGenerationAPI attribute) AsyncRequestLimiter (class in aoptk.literature.utils) authors (aoptk.literature.publication_metadata.PublicationMetadata attribute) aws_region (aoptk.literature.databases.pmc.PMC attribute)

B

batch_size (aoptk.literature.databases.pubmed.PubMed attribute)

bucket (aoptk.literature.databases.pmc.PMC attribute)

C

Causative (class in aoptk.relationship_type) chemical (aoptk.relationships.relationship.Relationship attribute) Chemical (class in aoptk.chemical) chemical_prompt_template (aoptk.text_generation_api.TextGenerationAPI attribute) client (aoptk.text_generation_api.TextGenerationAPI attribute) contains_any() (in module aoptk.text_utils) context (aoptk.relationships.relationship.Relationship attribute) convert_image() (aoptk.literature.convert_image.ConvertImage method) (aoptk.text_generation_api.TextGenerationAPI method)

convert_image_prompt_template (aoptk.text_generation_api.TextGenerationAPI attribute) convert_pdf_scan() (aoptk.literature.convert_pdf_scan.ConvertPDFScan method) (aoptk.text_generation_api.TextGenerationAPI method) convert_pdf_scan_prompt_template (aoptk.text_generation_api.TextGenerationAPI attribute) ConvertImage (class in aoptk.literature.convert_image) ConvertPDFScan (class in aoptk.literature.convert_pdf_scan) count (aoptk.literature.databases.pubmed.QueryTooLargeError attribute)

D

database (aoptk.literature.publication_metadata.PublicationMetadata attribute)

definition (aoptk.relationship_type.RelationshipType attribute) DOI (class in aoptk.literature.id)

E

effect (aoptk.relationships.relationship.Relationship attribute) Effect (class in aoptk.effect) end_of_span() (in module aoptk.text_utils)

ends() (in module aoptk.text_utils) endswith_digit() (in module aoptk.text_utils) EuropePMC (class in aoptk.literature.databases.europepmc)

F

figure_descriptions (aoptk.literature.publication.Publication attribute) figure_storage (aoptk.literature.databases.europepmc.EuropePMC attribute) (aoptk.literature.databases.pmc.PMC attribute) (aoptk.literature.pymupdf_parser.PymupdfParser attribute) figures (aoptk.literature.publication.Publication attribute) find_chemicals() (aoptk.find_chemical.FindChemical method) (aoptk.text_generation_api.TextGenerationAPI method) find_relationships_in_table() (aoptk.relationships.find_relationship.FindRelationship method) (aoptk.text_generation_api.TextGenerationAPI method) find_relationships_in_text() (aoptk.relationships.find_relationship.FindRelationship method) (aoptk.text_generation_api.TextGenerationAPI method)

find_relationships_in_text_and_images() (aoptk.relationships.find_relationship.FindRelationship method) (aoptk.text_generation_api.TextGenerationAPI method) find_relevant_publications() (aoptk.literature.find_relevant_publication.FindRelevantPublication method) (aoptk.text_generation_api.TextGenerationAPI method) find_relevant_publications_prompt_template (aoptk.text_generation_api.TextGenerationAPI attribute) FindChemical (class in aoptk.find_chemical) FindRelationship (class in aoptk.relationships.find_relationship) FindRelevantPublication (class in aoptk.literature.find_relevant_publication) full_text (aoptk.literature.publication.Publication attribute)

G

get_abstracts() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pubmed.PubMed method) (aoptk.literature.get_abstract.GetAbstract method) (aoptk.literature.pymupdf_parser.PymupdfParser method) get_ids() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pmc.PMC method) (aoptk.literature.databases.pubmed.PubMed method) (aoptk.literature.get_id.GetID method) get_pdfs() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pmc.PMC method) (aoptk.literature.get_pdf.GetPDF method) get_publication_count() (aoptk.literature.databases.pubmed.PubMed method)

get_publications() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pmc.PMC method) (aoptk.literature.get_publication.GetPublication method) (aoptk.literature.pymupdf_parser.PymupdfParser method) get_publications_metadata() (aoptk.literature.databases.europepmc.EuropePMC method) (aoptk.literature.databases.pubmed.PubMed method) (aoptk.literature.get_publication_metadata.GetPublicationMetadata method) GetAbstract (class in aoptk.literature.get_abstract) GetID (class in aoptk.literature.get_id) GetPDF (class in aoptk.literature.get_pdf) GetPublication (class in aoptk.literature.get_publication) GetPublicationMetadata (class in aoptk.literature.get_publication_metadata)

H

headers (aoptk.literature.databases.europepmc.EuropePMC attribute)

heading (aoptk.chemical.Chemical property)

I

id (aoptk.literature.abstract.Abstract attribute) (aoptk.literature.publication.Publication attribute) (aoptk.literature.publication_metadata.PublicationMetadata attribute) ID (class in aoptk.literature.id) id_list (aoptk.literature.databases.europepmc.EuropePMC attribute) (aoptk.literature.databases.pmc.PMC attribute) (aoptk.literature.databases.pubmed.PubMed attribute)

id_str (aoptk.literature.id.ID attribute) image_extensions (aoptk.literature.databases.europepmc.EuropePMC attribute) (aoptk.literature.databases.pmc.PMC attribute) Inhibitive (class in aoptk.relationship_type) is_europepmc_id() (in module aoptk.literature.utils)

L

limiter (aoptk.literature.databases.pmc.PMC attribute)

LLMFailureError

M

max_concurrency (aoptk.literature.databases.pmc.PMC attribute) max_pmc_results (aoptk.literature.databases.pmc.PMC attribute) max_requests_per_second (aoptk.literature.databases.pmc.PMC attribute) max_retries (aoptk.literature.databases.pubmed.PubMed attribute) maximum (aoptk.literature.databases.pubmed.QueryTooLargeError attribute) maximum_results (aoptk.literature.databases.pubmed.PubMed attribute) MeshTerms (class in aoptk.normalization.mesh_terms) min_interval (aoptk.literature.utils.AsyncRequestLimiter attribute) minimal_year_publication (aoptk.literature.databases.pmc.PMC attribute) model (aoptk.text_generation_api.TextGenerationAPI attribute) module aoptk aoptk.chemical aoptk.effect aoptk.find_chemical aoptk.literature aoptk.literature.abstract aoptk.literature.convert_image aoptk.literature.convert_pdf_scan aoptk.literature.databases aoptk.literature.databases.europepmc aoptk.literature.databases.pmc aoptk.literature.databases.pubmed aoptk.literature.find_relevant_publication aoptk.literature.get_abstract aoptk.literature.get_id aoptk.literature.get_pdf aoptk.literature.get_publication aoptk.literature.get_publication_metadata aoptk.literature.id aoptk.literature.pdf aoptk.literature.pdf_parser aoptk.literature.publication aoptk.literature.publication_metadata aoptk.literature.pymupdf_parser aoptk.literature.utils aoptk.normalization aoptk.normalization.mesh_terms aoptk.normalization.normalize_chemical aoptk.normalization.provide_mesh_term_dataframe_from_xml aoptk.normalization.provide_normalization_dataframe aoptk.normalization.pubchem_api aoptk.normalization.pubchem_local aoptk.relationship_type aoptk.relationships aoptk.relationships.find_relationship aoptk.relationships.relationship aoptk.text_generation_api aoptk.text_utils

N

name (aoptk.chemical.Chemical property) (aoptk.effect.Effect property) negative (aoptk.relationship_type.RelationshipType attribute) negative_verb (aoptk.relationship_type.RelationshipType attribute) normalization_prompt_template (aoptk.text_generation_api.TextGenerationAPI attribute)

normalize_chemical() (aoptk.normalization.mesh_terms.MeshTerms method) (aoptk.normalization.normalize_chemical.NormalizeChemical method) (aoptk.normalization.pubchem_api.PubChemAPI method) (aoptk.normalization.pubchem_local.PubChemSynonyms method) (aoptk.text_generation_api.TextGenerationAPI method) NormalizeChemical (class in aoptk.normalization.normalize_chemical)

P

page_size (aoptk.literature.databases.europepmc.EuropePMC attribute) paginator (aoptk.literature.databases.pmc.PMC attribute) path (aoptk.literature.pdf.PDF attribute) pattern_any_character (aoptk.literature.pymupdf_parser.PymupdfParser attribute) pattern_figure_descriptions (aoptk.literature.pymupdf_parser.PymupdfParser attribute) PDF (class in aoptk.literature.pdf) PDFParser (class in aoptk.literature.pdf_parser) pdfs (aoptk.literature.pymupdf_parser.PymupdfParser attribute) PMC (class in aoptk.literature.databases.pmc) PMCID (class in aoptk.literature.id) PMID (class in aoptk.literature.id) positive (aoptk.relationship_type.RelationshipType attribute) positive_verb (aoptk.relationship_type.RelationshipType attribute)

prompts_dir (aoptk.text_generation_api.TextGenerationAPI attribute) provide_normalization_dataframe() (aoptk.normalization.provide_mesh_term_dataframe_from_xml.ProvideMeshTermDataframeFromXML method) (aoptk.normalization.provide_normalization_dataframe.ProvideNormalizationDataframe method) ProvideMeshTermDataframeFromXML (class in aoptk.normalization.provide_mesh_term_dataframe_from_xml) ProvideNormalizationDataframe (class in aoptk.normalization.provide_normalization_dataframe) PubChemAPI (class in aoptk.normalization.pubchem_api) PubChemSynonyms (class in aoptk.normalization.pubchem_local) Publication (class in aoptk.literature.publication) publication_count (aoptk.literature.databases.pubmed.PubMed attribute) publication_date (aoptk.literature.publication_metadata.PublicationMetadata attribute) PublicationMetadata (class in aoptk.literature.publication_metadata) PubMed (class in aoptk.literature.databases.pubmed) PymupdfParser (class in aoptk.literature.pymupdf_parser)

Q

QueryTooLargeError

R

Relationship (class in aoptk.relationships.relationship) relationship_text_images_prompt_template (aoptk.text_generation_api.TextGenerationAPI attribute) relationship_text_prompt_template (aoptk.text_generation_api.TextGenerationAPI attribute) relationship_type (aoptk.relationships.relationship.Relationship attribute)

relationships_table_prompt_template (aoptk.text_generation_api.TextGenerationAPI attribute) RelationshipType (class in aoptk.relationship_type) remove_reviews() (aoptk.literature.databases.europepmc.EuropePMC method) retries (aoptk.literature.databases.pmc.PMC attribute) role (aoptk.text_generation_api.TextGenerationAPI attribute)

S

s3 (aoptk.literature.databases.pmc.PMC attribute) search_date (aoptk.literature.publication_metadata.PublicationMetadata attribute) semaphore (aoptk.literature.databases.pmc.PMC attribute) similar() (aoptk.chemical.Chemical method)

specification_relationship_text_prompt (aoptk.text_generation_api.TextGenerationAPI attribute) storage (aoptk.literature.databases.europepmc.EuropePMC attribute) (aoptk.literature.databases.pmc.PMC attribute) synonyms (aoptk.chemical.Chemical property)

T

tables (aoptk.literature.publication.Publication attribute) temperature (aoptk.text_generation_api.TextGenerationAPI attribute) text (aoptk.literature.abstract.Abstract attribute) text_generation (aoptk.literature.pymupdf_parser.PymupdfParser attribute) TextGenerationAPI (class in aoptk.text_generation_api)

timeout (aoptk.literature.databases.europepmc.EuropePMC attribute) (aoptk.normalization.pubchem_api.PubChemAPI attribute) title (aoptk.literature.publication_metadata.PublicationMetadata attribute) top_p (aoptk.text_generation_api.TextGenerationAPI attribute) topics (in module aoptk.text_generation_api)

U

url (aoptk.text_generation_api.TextGenerationAPI attribute)

W

wait_turn() (aoptk.literature.utils.AsyncRequestLimiter method)