Sci Paper Reviewer

=3.9 Document parsing libraries (optional but supported): pypdf (version varies) pdfplumber (version varies) PyMuPDF (version varies) PyPDF2 (version varies) python-docx (version varies) The parser should fall back to basic extraction if some advanced libraries are unavailable. Example Usage

1. Parse a file and review the extracted text

Parse an uploaded manuscript into a text file (recommended to avoid console buffer limits)

python scripts/enhanced_document_parser.py /path/to/manuscript.pdf extracted_content.txt Then provide extracted_content.txt to the skill (or paste its content) and request a review, for example: Please review this manuscript as a strict SCI reviewer. Requirements:

1. Classify research type.
2. Evaluate innovation (score 1–12) using your rubric.
3. Screen Results for logic vulnerabilities (false positives, mechanism breaks, control failures).
4. Output a structured report with numbered experimental modification suggestions. [PASTE CONTENT OF extracted_content.txt HERE]
5. Direct text input (no file) I will paste the manuscript text below. Please perform an SCI-style review:

• Extract Abstract/Results/Introduction/Discussion (as available)
• Classify research type
• Innovation score (1–12) and rationale
• Logic vulnerability screening
• Provide numbered modification suggestions only (no generic “other suggestions”) [PASTE MANUSCRIPT TEXT] Implementation Details

1. Document Processing Rules Input detection : If a file is provided, detect type: PDF , DOCX , DOC , or TXT . If text is pasted, process it directly. Parsing script : Use: scripts/enhanced_document_parser.py Recommended invocation (write to file): python scripts/enhanced_document_parser.py <file_path> extracted_content.txt Then read extracted_content.txt as the canonical extracted content. Failure handling : If the parser outputs Warning: No text extracted , treat the file as likely scanned/image-based and inform the user that OCR may be required before review.
2. Section Extraction (for analysis) From the parsed content, extract (as available): Abstract (work summary) Results (core experimental findings and data claims) Introduction & Discussion (background, positioning, interpretation) If headings are missing, infer sections by typical academic structure and transitions.
3. Research Type Classification Classify into one of: Materials Research Basic Medical Research Clinical Research Review Use cues such as study subjects (cells/animals/patients), endpoints, materials synthesis/characterization, and whether the manuscript is primarily summarizing prior work.
4. Innovation Evaluation (Score 1–12) Evaluate primarily from Introduction and Discussion (and claims in Abstract), using the following rubric: Major Original (9–12) : Proposes a fundamentally new mechanism or a disruptive hypothesis. Clear Translation Path (8–11) : Identifies targetable markers and provides inhibitor screening/validation data. Theory Extension (5–8) : Extends the boundary or applicability of an existing theory/framework. Potential Application Value (4–7) : Reveals regulatory mechanisms but lacks actionable intervention/translation. Validation Study (1–4) : Primarily replicates/validates known theories or fills incremental details. Heuristic note : “miRNA-based novelty” is generally treated as average unless supported by strong mechanistic and translational evidence.
5. Logic Vulnerability Screening (Results-Focused) Screen the Results for the following vulnerabilities: False Positive Risk Claims rely on a single assay/marker without orthogonal validation (e.g., only qPCR without protein-level confirmation; only one antibody without specificity checks). Mechanism Break Upstream/downstream relationships are asserted but not experimentally verified (e.g., correlation presented as causation; missing rescue/epistasis tests). Control Failure Key experiments lack appropriate controls, especially double-negative controls where required (e.g., vehicle + non-targeting controls; isotype controls; sham operations; matched baseline). Basic Medicine Rule (method sufficiency) For cell-level knockdown, siRNA/shRNA is sufficient ; CRISPR is not mandatory unless the claim requires stable knockout or allele-specific inference.
6. Required Output Structure (Final Review Report) The generated review must follow this structure: Document Information File type and processing status Extracted sections overview (what was found/used) Parser used (enhanced parser vs. fallback) Innovation Evaluation Provide the innovation level and rationale (score may be stated explicitly or implied, but must map to the rubric). Use academic, precise language. Experimental Modification Suggestions Provide only concrete, logic-driven revisions derived from the vulnerability screening. Number items as 2.1, 2.2, 2.3, ... Avoid generic “Other suggestions”; each item must specify what experiment/control/verification to add and what claim it would support or falsify.