Index

_

__init__() (metapub.base.Borg method) (metapub.base.MetaPubObject method) (metapub.ClinVarFetcher method), [1] (metapub.clinvarfetcher.ClinVarFetcher method) (metapub.ClinVarVariant method) (metapub.clinvarvariant.ClinVarVariant method) (metapub.clinvarvariant.PathogenicSummary method) (metapub.crossref.CrossRefFetcher method) (metapub.crossref.CrossRefWork method) (metapub.CrossRefFetcher method) (metapub.dx_doi.DxDOI method) (metapub.exceptions.AccessDenied method) (metapub.exceptions.BadDOI method) (metapub.exceptions.BaseXMLError method) (metapub.exceptions.CrossRefConnectionError method) (metapub.exceptions.DxDOIError method) (metapub.exceptions.InvalidBookID method) (metapub.exceptions.InvalidPMID method) (metapub.exceptions.MetaPubError method) (metapub.exceptions.NoPDFLink method) (metapub.findit.findit.FindIt method) (metapub.MedGenConcept method) (metapub.medgenconcept.MedGenConcept method) (metapub.MedGenFetcher method), [1] (metapub.medgenfetcher.MedGenFetcher method) (metapub.ncbi_errors.NCBIErrorDetector method) (metapub.ncbi_errors.NCBIServiceError method) (metapub.ncbi_errors.ServiceStatus method) (metapub.ncbi_health_check.NCBIHealthChecker method) (metapub.ncbi_health_check.ServiceResult method) (metapub.PubMedArticle method), [1] (metapub.pubmedarticle.PubMedArticle method) (metapub.PubMedAuthor method) (metapub.pubmedauthor.PubMedAuthor method) (metapub.PubMedFetcher method), [1] (metapub.pubmedfetcher.PubMedFetcher method) (metapub.urlreverse.urlreverse.UrlReverse method)

A

AccessDenied add_note() (metapub.exceptions.AccessDenied method) (metapub.exceptions.BadDOI method) (metapub.exceptions.BaseXMLError method) (metapub.exceptions.CrossRefConnectionError method) (metapub.exceptions.DxDOIError method) (metapub.exceptions.InvalidBookID method) (metapub.exceptions.InvalidPMID method) (metapub.exceptions.MetaPubError method) (metapub.exceptions.NoPDFLink method) (metapub.ncbi_errors.NCBIServiceError method) args (metapub.exceptions.AccessDenied attribute) (metapub.exceptions.BadDOI attribute) (metapub.exceptions.BaseXMLError attribute) (metapub.exceptions.CrossRefConnectionError attribute) (metapub.exceptions.DxDOIError attribute) (metapub.exceptions.InvalidBookID attribute) (metapub.exceptions.InvalidPMID attribute) (metapub.exceptions.MetaPubError attribute) (metapub.exceptions.NoPDFLink attribute) (metapub.ncbi_errors.NCBIServiceError attribute)

article() (in module metapub.cite) article_by_doi() (metapub.crossref.CrossRefFetcher method) (metapub.CrossRefFetcher method) article_by_pma() (metapub.crossref.CrossRefFetcher method) (metapub.CrossRefFetcher method) article_by_title() (metapub.crossref.CrossRefFetcher method) (metapub.CrossRefFetcher method) asciify() (in module metapub.utils) assert_is_good_doi() (in module metapub.validate) assert_is_good_pmid() (in module metapub.validate) author1 (metapub.crossref.CrossRefWork property) author1_last_fm (metapub.crossref.CrossRefWork property) author_list (metapub.crossref.CrossRefWork property) author_list_last_fm (metapub.crossref.CrossRefWork property) author_str() (in module metapub.cite) authors_str_lastfirst (metapub.crossref.CrossRefWork property)

B

BadDOI BaseXMLError bibtex() (in module metapub.cite)

book() (in module metapub.cite) bookid2pmid() (in module metapub.convert) Borg (class in metapub.base)

C

check_all_services() (metapub.ncbi_health_check.NCBIHealthChecker method) check_doi() (metapub.dx_doi.DxDOI method), [1] check_ncbi_status() (in module metapub.ncbi_errors) check_service() (metapub.ncbi_health_check.NCBIHealthChecker method) check_service_status() (metapub.ncbi_errors.NCBIErrorDetector method) citation (metapub.crossref.CrossRefWork property) (metapub.PubMedArticle property), [1] (metapub.pubmedarticle.PubMedArticle property) citation() (in module metapub.cite) citation_bibtex (metapub.PubMedArticle property) (metapub.pubmedarticle.PubMedArticle property) citation_html (metapub.PubMedArticle property), [1] (metapub.pubmedarticle.PubMedArticle property)

cleanup_dir() (in module metapub.cache_utils) ClinVarFetcher (class in metapub) (class in metapub.clinvarfetcher) ClinVarVariant (class in metapub) (class in metapub.clinvarvariant) conflicting (metapub.clinvarvariant.PathogenicSummary attribute) consensus (metapub.clinvarvariant.PathogenicSummary attribute) counts (metapub.clinvarvariant.PathogenicSummary attribute) CrossRefConnectionError CrossRefFetcher (class in metapub) (class in metapub.crossref) CrossRefWork (class in metapub.crossref)

D

datetime_to_timestamp() (in module metapub.cache_utils) deparameterize() (in module metapub.utils) details (metapub.ncbi_health_check.ServiceResult attribute) determine_pubmed_xml_type() (in module metapub.pubmedarticle) diagnose_error() (metapub.ncbi_errors.NCBIErrorDetector method)

diagnose_ncbi_error() (in module metapub.ncbi_errors) doi2pmid() (in module metapub.convert), [1] DxDOI (class in metapub.dx_doi) DXDOI() (in module metapub.urlreverse.methods) DxDOIError

E

error_message (metapub.ncbi_errors.ServiceStatus attribute) (metapub.ncbi_health_check.ServiceResult attribute)

error_type (metapub.ncbi_errors.ServiceStatus attribute)

F

find_article_from_doi() (in module metapub.findit.logic) find_article_from_pma() (in module metapub.findit.logic) find_doi_in_string() (in module metapub.text_mining) findall_dois_in_text() (in module metapub.text_mining)

findall_ncbi_bookIDs() (in module metapub.text_mining) findall_pmcIDs() (in module metapub.text_mining) FindIt (class in metapub.findit.findit) first_page (metapub.crossref.CrossRefWork property) format_user_error() (in module metapub.ncbi_errors)

G

get_ahajournals_doi_from_link() (in module metapub.urlreverse.methods) get_article_info_from_url() (in module metapub.urlreverse.urlreverse) get_biomedcentral_doi_from_link() (in module metapub.urlreverse.methods) get_bmj_doi_from_link() (in module metapub.urlreverse.methods) get_cache_path() (in module metapub.cache_utils) get_cell_doi_from_link() (in module metapub.urlreverse.methods) get_data_log() (in module metapub.config) get_doi_for_otherid() (in module metapub.pubmedcentral) get_early_release_doi_from_link() (in module metapub.urlreverse.methods) get_elifesciences_doi_from_link() (in module metapub.urlreverse.methods) get_eutils_client() (in module metapub.eutils_common) get_generic_doi_from_link() (in module metapub.urlreverse.methods) get_jci_doi_from_link() (in module metapub.urlreverse.methods)

get_journal_name_from_url() (in module metapub.urlreverse.methods) get_jstage_doi_from_link() (in module metapub.urlreverse.methods) get_karger_doi_from_link() (in module metapub.urlreverse.methods) get_most_similar_work_from_crossref_results() (in module metapub.crossref) get_nature_doi_from_link() (in module metapub.urlreverse.methods) get_plos_doi_from_link() (in module metapub.urlreverse.methods) get_pmc_fulltext_filename_for_PubMedArticle() (in module metapub.text_mining) get_pmcid_for_otherid() (in module metapub.pubmedcentral) get_pmid_for_otherid() (in module metapub.pubmedcentral) get_pnas_doi_from_link() (in module metapub.urlreverse.methods) get_process_log() (in module metapub.config) get_sciencedirect_doi_from_link() (in module metapub.urlreverse.methods) get_spandidos_doi_from_link() (in module metapub.urlreverse.methods) get_uids_from_esearch_result() (in module metapub.pubmedfetcher)

H

handle_ncbi_request_error() (in module metapub.ncbi_errors) hgvs_c (metapub.ClinVarVariant property) (metapub.clinvarvariant.ClinVarVariant property) hgvs_g (metapub.ClinVarVariant property) (metapub.clinvarvariant.ClinVarVariant property)

hgvs_p (metapub.ClinVarVariant property) (metapub.clinvarvariant.ClinVarVariant property) hostname_of() (in module metapub.utils)

I

interpret_pmids_for_citation_results() (in module metapub.convert) InvalidBookID InvalidPMID

is_available (metapub.ncbi_errors.ServiceStatus attribute) is_ncbi_bookID() (in module metapub.text_mining) is_pmcid() (in module metapub.text_mining)

K

kpick() (in module metapub.utils)

L

load() (metapub.findit.findit.FindIt method) load_from_cache() (metapub.findit.findit.FindIt method)

log (in module metapub.findit.findit) lowercase_keys() (in module metapub.utils)

M

main() (in module metapub.convert) (in module metapub.ncbi_health_check) (in module metapub.pubmedfetcher_cli) medgen_uid (metapub.MedGenConcept property) (metapub.medgenconcept.MedGenConcept property) MedGenConcept (class in metapub) (class in metapub.medgenconcept) MedGenFetcher (class in metapub) (class in metapub.medgenfetcher) metapub module metapub.base module metapub.cache_utils module metapub.cite module metapub.clinvarfetcher module metapub.clinvarvariant module metapub.config module metapub.convert module metapub.crossref module metapub.dx_doi module metapub.eutils_common module metapub.exceptions module metapub.findit module metapub.findit.dances module metapub.findit.findit module metapub.findit.journals module metapub.findit.logic module metapub.medgenconcept module metapub.medgenfetcher module metapub.ncbi_errors module metapub.ncbi_health_check module metapub.pubmed_clinicalqueries module metapub.pubmedarticle module metapub.pubmedauthor module metapub.pubmedcentral module

metapub.pubmedfetcher module metapub.pubmedfetcher_cli module metapub.text_mining module metapub.urlreverse module metapub.urlreverse.hostname2doiprefix module metapub.urlreverse.hostname2jrnl module metapub.urlreverse.methods module metapub.urlreverse.urlreverse module metapub.utils module metapub.validate module MetaPubError MetaPubObject (class in metapub.base) module metapub metapub.base metapub.cache_utils metapub.cite metapub.clinvarfetcher metapub.clinvarvariant metapub.config metapub.convert metapub.crossref metapub.dx_doi metapub.eutils_common metapub.exceptions metapub.findit metapub.findit.dances metapub.findit.findit metapub.findit.journals metapub.findit.logic metapub.medgenconcept metapub.medgenfetcher metapub.ncbi_errors metapub.ncbi_health_check metapub.pubmed_clinicalqueries metapub.pubmedarticle metapub.pubmedauthor metapub.pubmedcentral metapub.pubmedfetcher metapub.pubmedfetcher_cli metapub.text_mining metapub.urlreverse metapub.urlreverse.hostname2doiprefix metapub.urlreverse.hostname2jrnl metapub.urlreverse.methods metapub.urlreverse.urlreverse metapub.utils metapub.validate

N

name (metapub.ncbi_health_check.ServiceResult attribute) NCBIErrorDetector (class in metapub.ncbi_errors)

NCBIHealthChecker (class in metapub.ncbi_health_check) NCBIServiceError NoPDFLink

P

parameterize() (in module metapub.utils) parse_elink_response() (in module metapub.base) parse_related_pmids_result() (in module metapub.pubmedfetcher) parse_xml() (metapub.base.MetaPubObject static method) (metapub.ClinVarVariant static method) (metapub.clinvarvariant.ClinVarVariant static method) (metapub.MedGenConcept static method) (metapub.medgenconcept.MedGenConcept static method) (metapub.PubMedArticle static method) (metapub.pubmedarticle.PubMedArticle static method) (metapub.PubMedAuthor static method) (metapub.pubmedauthor.PubMedAuthor static method) PathogenicSummary (class in metapub.clinvarvariant) pick_pmid() (in module metapub.text_mining) pmid2doi() (in module metapub.convert), [1] pmid_for_bookID() (metapub.PubMedFetcher method) (metapub.pubmedfetcher.PubMedFetcher method) pmids_for_citation() (metapub.PubMedFetcher method), [1] (metapub.pubmedfetcher.PubMedFetcher method)

pmids_for_clinical_query() (metapub.PubMedFetcher method) (metapub.pubmedfetcher.PubMedFetcher method) pmids_for_medical_genetics_query() (metapub.PubMedFetcher method) (metapub.pubmedfetcher.PubMedFetcher method) print_pma() (in module metapub.pubmedfetcher_cli) print_results() (in module metapub.ncbi_health_check) print_status_icon() (in module metapub.ncbi_health_check) pubdate (metapub.crossref.CrossRefWork property) (metapub.PubMedArticle property) (metapub.pubmedarticle.PubMedArticle property) PubMedArticle (class in metapub) (class in metapub.pubmedarticle) PubMedArticle2doi() (in module metapub.convert) PubMedAuthor (class in metapub) (class in metapub.pubmedauthor) PubMedFetcher (class in metapub) (class in metapub.pubmedfetcher) pubmonth (metapub.crossref.CrossRefWork property) pubyear (metapub.crossref.CrossRefWork property)

R

related_pmids() (metapub.PubMedFetcher method), [1] (metapub.pubmedfetcher.PubMedFetcher method) remove_chars() (in module metapub.utils) remove_html_markup() (in module metapub.utils)

resolve() (metapub.dx_doi.DxDOI method), [1] response_time (metapub.ncbi_errors.ServiceStatus attribute) (metapub.ncbi_health_check.ServiceResult attribute) review_status (metapub.clinvarvariant.PathogenicSummary attribute) rootdomain_of() (in module metapub.utils)

S

scrape_doi_from_article_page() (in module metapub.text_mining) ServiceResult (class in metapub.ncbi_health_check) ServiceStatus (class in metapub.ncbi_errors) square_voliss_data_for_pma() (in module metapub.pubmedarticle) squash_spaces() (in module metapub.utils)

status (metapub.ncbi_health_check.ServiceResult attribute) status_code (metapub.ncbi_errors.ServiceStatus attribute) (metapub.ncbi_health_check.ServiceResult attribute) synonyms (metapub.MedGenConcept property) (metapub.medgenconcept.MedGenConcept property)

T

to_citation() (metapub.crossref.CrossRefWork method) to_dict() (metapub.ClinVarVariant method) (metapub.clinvarvariant.ClinVarVariant method) (metapub.crossref.CrossRefWork method) (metapub.findit.findit.FindIt method) (metapub.MedGenConcept method) (metapub.medgenconcept.MedGenConcept method) (metapub.PubMedArticle method), [1] (metapub.pubmedarticle.PubMedArticle method) (metapub.PubMedAuthor method) (metapub.pubmedauthor.PubMedAuthor method) (metapub.urlreverse.urlreverse.UrlReverse method)

total_submitters (metapub.clinvarvariant.PathogenicSummary attribute) try_doi_methods() (in module metapub.urlreverse.methods) try_pmid_methods() (in module metapub.urlreverse.methods) try_vip_methods() (in module metapub.urlreverse.methods)

U

url (metapub.ncbi_health_check.ServiceResult attribute)

UrlReverse (class in metapub.urlreverse.urlreverse)

W

with_traceback() (metapub.exceptions.AccessDenied method) (metapub.exceptions.BadDOI method) (metapub.exceptions.BaseXMLError method) (metapub.exceptions.CrossRefConnectionError method) (metapub.exceptions.DxDOIError method) (metapub.exceptions.InvalidBookID method) (metapub.exceptions.InvalidPMID method) (metapub.exceptions.MetaPubError method) (metapub.exceptions.NoPDFLink method) (metapub.ncbi_errors.NCBIServiceError method)