jp_comment_report.csv

file,line_or_cell,snippet
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_prod_plus_transformers.ipynb,cell6:line3,nltk.download('punkt')       # 既に入っていてもOK
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_prod_plus_transformers.ipynb,cell6:line4,nltk.download('punkt_tab')   # ★ これが新たに必要
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell1:line3,"PMCID がある被引用論文では、**JATS の `<ref-list>` と `<xref ref-type=""bibr"">`** を突き合わせ、"
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell1:line4,対象論文（PMID/DOI）に対応する **実引用文** を抽出します。PMCID がない場合は抄録にフォールバックできます。
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell2:line2,- `TARGET_PMID`: 解析対象の PMID
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell2:line3,- `OUT_DIR`: 出力先
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell2:line4,- `MAX_CITING`: 被引用の最大件数（None で全件）
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell2:line5,- `FALLBACK_TO_ABSTRACT`: True なら PMC で見つからない時に抄録で代替
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell2:line6,- `NCBI_API_KEY`: 任意。設定すると 3 req/s → 10 req/s
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell2:line7,- `PAUSE`: API 呼び出し間隔（秒）
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell4:line2,`punkt_tab` は NLTK 3.8+ で必要です。
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell7:line2,1) `efetch` で対象メタ → 2) `elink` で Cited‑by PMIDs → 3) citing の PMCID があれば JATS を取得
BDBRA-build-v2/src/relaiblity_score/citation_sentiment_refaware_basic_v2.ipynb,cell7:line3,4) `<ref-list>` で対象の `<ref id>` を特定 → 5) `<xref>` から本文側の**文**を抽出 → 6) スコアリングして CSV
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,312,"""クエリを入力してください。"")"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,700,"return gr.update(value=""Sender と Receiver を入力/選択してください。""), empty, empty, empty, empty"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,706,"return gr.update(value=f""**未存在**：Connections に `{sender}` → `{receiver}` の行はありません。""), empty, empty, empty, empty"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,709,"msg = gr.update(value=f""**存在します**：`{sender}` → `{receiver}`（connections: {len(df_conn)} 件）"")"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,745,"return (gr.update(value=""領域を選択してください。""),"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,760,"msg = f""選択: `{rid}` — as **Sender**: {cnt_s} 件 / as **Receiver**: {cnt_r} 件"""
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,806,"return (gr.update(value=""領域を先に選択してください。""), empty, empty, empty, empty)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,820,"return (gr.update(value=""対向候補を選択してください。""), empty, empty, empty, empty)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,827,"return (gr.update(value=""表示をクリアしました。""), empty, empty, empty, empty)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,845,"query = gr.Textbox(label=""キーワード"", placeholder=""2文字以上でサジェスト"", scale=4)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,846,"limit = gr.Slider(label=""最大件数"", minimum=5, maximum=100, value=20, step=5, scale=1)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,850,"suggest = gr.Dropdown(label=""候補 Circuit ID"", choices=[], interactive=True, allow_custom_value=False)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,852,"diag = gr.Code(label=""診断情報"", interactive=False)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,854,"with gr.Accordion(""A. Circuit に類似"", open=True):"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,861,"with gr.Accordion(""B. Receiver に類似"", open=True):"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,888,"sender_q = gr.Textbox(label=""Sender (Circuit ID)"", placeholder=""2文字以上でサジェスト"", scale=3)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,889,"receiver_q = gr.Textbox(label=""Receiver (Receiver ID)"", placeholder=""2文字以上でサジェスト"", scale=3)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,894,"suggest_sender = gr.Dropdown(label=""候補（Circuit ID）"", choices=[], interactive=True, allow_custom_value=False)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,895,"suggest_receiver = gr.Dropdown(label=""候補（Receiver ID）"", choices=[], interactive=True, allow_custom_value=False)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,924,"region_text = gr.Textbox(label=""領域（ID/Names/Receiver）"", placeholder=""2文字以上でサジェスト"", scale=3)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,925,"region_suggest = gr.Dropdown(label=""候補（クリックで確定）"", choices=[], interactive=True, allow_custom_value=False, scale=2)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,926,"mode = gr.Radio(label=""方向"", choices=[""Auto"",""Use as Sender"",""Use as Receiver""], value=""Auto"", scale=2)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,929,"receivers_dd = gr.Dropdown(label=""対向候補（あなたが Sender のときの Receivers）"", choices=[], interactive=False, allow_custom_value=False)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,930,"senders_dd   = gr.Dropdown(label=""対向候補（あなたが Receiver のときの Senders）"", choices=[], interactive=False, allow_custom_value=False)"
BDBRA-build-v2/src/vis_tool/gradio_wholebif_query_app_flexpair_public_v2_fix2.py,968,"gr.Markdown(""— ヒント: `CREATE EXTENSION IF NOT EXISTS pg_trgm;` を有効にするとサジェスト/検索の精度が上がります。—"")"
BDBRA-build-v2/src/neural_projection_bundle/NeuralProjection_Colab.ipynb,cell1:line2,改良版：Methodハイブリッド推定 + DOI補完 + 強化プロンプト
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,7,超高速化ポイント（--fast 時）:
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,8,- Europe PMC / Crossref 照会を完全スキップ
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,9,- MeSH UI / Tree のルックアップをスキップ
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,10,- Taxonomy ID 解決をスキップ（ラベル抽出のみ）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,11,- PubMed History(WebEnv) を使わず、ESearch で ID をページング → ESummary & EFetch by IDs
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,12,"- 既定: chunk=1000, sleep=0.1（API key がある前提。混雑時は上げてください）"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,14,通常モード（--fast なし）:
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,15,- 以前の nofulltext 版と同等（EuropePMC/Crossref/MeSH enrich/TaxID 有効）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,16,- ただし、TaxID/MeSH の結果はメモリキャッシュして重複呼び出しを削減
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,18,出力列は nofulltext と同一:
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,401,"ap.add_argument(""--fast"", action=""store_true"", help=""極力速く（OA/Crossref/MeSH enrich/TaxIDをスキップし、IDページング方式に）"")"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,402,"ap.add_argument(""--no_history"", action=""store_true"", help=""履歴(WebEnv)を使わず ID ページングする"")"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,403,"ap.add_argument(""--no_epmc"", action=""store_true"", help=""EuropePMC 照会を行わない"")"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,404,"ap.add_argument(""--no_crossref"", action=""store_true"", help=""Crossref 照会を行わない"")"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,405,"ap.add_argument(""--no_mesh_enrich"", action=""store_true"", help=""MeSH UI/Tree 付与を行わない"")"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast.py,406,"ap.add_argument(""--no_taxonomy_ids"", action=""store_true"", help=""Taxonomy ID 解決を行わない（ラベル抽出のみ）"")"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,6,変更点（要旨）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,7,- ESearch を Biopython ではなく **requests の POST + JSON** に切替（URL長と400を回避）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,8,- PDAT 範囲はクエリ term に埋め込み（param の datetype/mindate/maxdate は不使用）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,9,"- 大量件数は PDAT 自動二分割でキャップ（既定 9,000 件/スライス）→ ID ページング"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,10,- 本文取得はしない（EFetch はアブストラクト等のメタ用に XML 取得のみ）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,11,- 高密度日スライスのみ、必要に応じて **履歴方式(usehistory=y)へフォールバック**可
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,13,出力列（CSV）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,14,"title, doi(httpsリンク), pmid, journal, abstract,"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,15,"taxon_labels（ラベルのみ）, taxon_ncbi_ids（空欄）, taxon_source,"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,16,"pmcid, oa_url（空欄）, oa_license（空欄）, publisher_url（空欄）, publisher_license（空欄）,"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,17,"mesh_ui（空欄）, mesh_tree_numbers（空欄）"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,36,# 語彙（ベース）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,96,# クエリ整形 & PDAT 範囲
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,104,# スペース無しのコロンで安定化（400回避の経験則）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,108,# E-utilities POST (JSON) ヘルパ
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,160,# 履歴（必要時フォールバック）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,172,# ESummary は Biopython（POST使用・XML→Python）で十分安定
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,194,# PubMed XML パース & Taxon（ラベルのみ）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,332,# PDAT 分割
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,363,# 1行書き出し
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,423,# メイン
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,436,"ap.add_argument(""--fast"", action=""store_true"", help=""外部照会はせず最速で収集"")"
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,443,# 既定（--fast は攻め）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,451,# Entrez 設定（requests 側も _common_params() で活用）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,456,# クエリ構築
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,472,# 期間
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,478,# 再開用（既存PMID）
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,490,# スライス作成
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,501,# 高密度日 → 履歴方式
BDBRA-build-v2/src/hav_pubmed/harvest_pubmed_projections_pro_nofulltext_fast_split_2.py,540,# 通常スライス：ID ページング