Annotation System Flags¶

Complete documentation for article annotation and organization flags

Table of Contents¶

Overview
Creating Annotations
Viewing Annotations
Managing Annotations
Annotation Workflows

Overview¶

The annotation system allows you to rate, tag, comment on, and organize research articles for better literature management.

Total Annotation Flags: 13

Features: - 5-star rating system - Comments and notes - Tag organization - Read status tracking (unread, reading, read) - Priority levels (low, medium, high)

Storage: Annotations saved in ~/.lixplore_annotations.json

Creating Annotations¶

`--annotate`¶

Description: Annotate specific article from last search.

Syntax:

lixplore --annotate N [--comment TEXT] [--rating 1-5] [--tags TAGS] [--read-status STATUS] [--priority LEVEL]

Type: Integer (article number)

Examples¶

Example 1: Basic Annotation

# Search first
lixplore -P -q "cancer treatment" -m 20

# Annotate article #5
lixplore --annotate 5 --rating 5 --tags "important,methodology"

Example 2: Full Annotation

lixplore --annotate 3 \
  --rating 4 \
  --tags "review,cite-in-paper" \
  --comment "Excellent methodology section, relevant for my research" \
  --read-status reading \
  --priority high

Example 3: Quick Rating

lixplore --annotate 7 --rating 5

Example 4: Add Comment Only

lixplore --annotate 2 --comment "Follow up on this author's other work"

Example 5: Mark as Read

lixplore --annotate 10 --read-status read

Example 6: Set Priority

lixplore --annotate 1 --priority high --tags "must-read"

Example 7: Multiple Tags

lixplore --annotate 4 --tags "methodology,statistics,cite,review-later"

Example 8: Update Existing Annotation

# Add to existing annotation
lixplore --annotate 5 --comment "Additional notes after reading" --read-status read

`--comment`¶

Description: Add comment/note to article (use with --annotate).

Syntax:

lixplore --annotate N --comment "TEXT"

Type: String value

Examples¶

Example 1: Research Note

lixplore --annotate 3 --comment "Key findings: p < 0.001 for intervention group"

Example 2: Methodology Note

lixplore --annotate 5 --comment "Uses novel statistical approach - investigate further"

Example 3: Citation Reminder

lixplore --annotate 7 --comment "Cite in introduction, relevant background"

`--rating`¶

Description: Rate article 1-5 stars (use with --annotate).

Syntax:

lixplore --annotate N --rating [1-5]

Type: Integer (1-5)

Examples¶

Example 1: Excellent Paper

lixplore --annotate 2 --rating 5 --tags "excellent,must-cite"

Example 2: Good Reference

lixplore --annotate 8 --rating 4

Example 3: Poor Quality

lixplore --annotate 12 --rating 2 --comment "Weak methodology"

Rating Guide: - ⭐⭐⭐⭐⭐ (5) - Excellent, must-cite - ⭐⭐⭐⭐ (4) - Very good, relevant - ⭐⭐⭐ (3) - Good, useful reference - ⭐⭐ (2) - Fair, limited usefulness - ⭐ (1) - Poor quality

`--tags`¶

Description: Add comma-separated tags (use with --annotate).

Syntax:

lixplore --annotate N --tags "TAG1,TAG2,TAG3"

Type: Comma-separated string

Examples¶

Example 1: Research Tags

lixplore --annotate 3 --tags "methodology,statistics,relevant"

Example 2: Organization Tags

lixplore --annotate 5 --tags "chapter2,lit-review,must-cite"

Example 3: Action Tags

lixplore --annotate 7 --tags "read-later,print,discuss-with-advisor"

Example 4: Topic Tags

lixplore --annotate 9 --tags "machine-learning,healthcare,predictive-models"

Suggested Tag Categories: - Importance: important, must-read, must-cite, key-paper - Topic: methodology, results, review, meta-analysis - Action: read-later, print, email, discuss - Project: chapter1, chapter2, introduction, discussion - Quality: excellent, good, questionable, weak-methods

`--read-status`¶

Description: Set read status (use with --annotate).

Syntax:

lixplore --annotate N --read-status [unread|reading|read]

Type: String choice

Options: - unread - Not yet started - reading - Currently reading - read - Completed

Examples¶

Example 1: Mark as Reading

lixplore --annotate 5 --read-status reading

Example 2: Mark as Read with Rating

lixplore --annotate 3 --read-status read --rating 5

Example 3: Unread Priority

lixplore --annotate 7 --read-status unread --priority high

`--priority`¶

Description: Set priority level (use with --annotate).

Syntax:

lixplore --annotate N --priority [low|medium|high]

Type: String choice

Options: - high - Must read soon - medium - Normal priority (default) - low - Read if time permits

Examples¶

Example 1: High Priority

lixplore --annotate 2 --priority high --tags "deadline,important"

Example 2: Low Priority

lixplore --annotate 10 --priority low --read-status unread

Viewing Annotations¶

`--show-annotation`¶

Description: Show annotation for specific article.

Syntax:

lixplore --show-annotation N

Type: Integer (article number from last search)

Examples¶

Example 1: View Annotation

# Search first
lixplore -P -q "cancer" -m 20

# View annotation for article #5
lixplore --show-annotation 5

Example 2: Check Before Update

lixplore --show-annotation 3
# Then update:
lixplore --annotate 3 --comment "Additional notes"

`--list-annotations`¶

Description: List all annotated articles.

Syntax:

lixplore --list-annotations

Type: Boolean flag

Examples¶

Example 1: View All Annotations

lixplore --list-annotations

Example 2: Filter High Priority

lixplore --filter-annotations "priority=high"

`--filter-annotations`¶

Description: Filter annotations by criteria.

Syntax:

lixplore --filter-annotations "KEY=VALUE,KEY=VALUE"

Type: String (comma-separated filters)

Filter Keys: - min_rating - Minimum rating (1-5) - max_rating - Maximum rating (1-5) - read_status - Read status (unread, reading, read) - priority - Priority level (low, medium, high) - tag - Tag name (must contain tag)

Examples¶

Example 1: High-Rated Papers

lixplore --filter-annotations "min_rating=4"

Example 2: High Priority Unread

lixplore --filter-annotations "priority=high,read_status=unread"

Example 3: Specific Tag

lixplore --filter-annotations "tag=must-cite"

Example 4: Reading List

lixplore --filter-annotations "read_status=reading"

Example 5: Excellence Filter

lixplore --filter-annotations "min_rating=5,priority=high"

Example 6: Multiple Criteria

lixplore --filter-annotations "min_rating=4,read_status=read,priority=high"

`--search-annotations`¶

Description: Search annotations by keyword.

Syntax:

lixplore --search-annotations "KEYWORD"

Type: String value

Searches In: - Article titles - Comments/notes - Tags

Examples¶

Example 1: Search Comments

lixplore --search-annotations "methodology"

Example 2: Search Tags

lixplore --search-annotations "machine-learning"

Example 3: Search Titles

lixplore --search-annotations "CRISPR"

Managing Annotations¶

`--export-annotations`¶

Description: Export all annotations to file.

Syntax:

lixplore --export-annotations [markdown|json|csv]

Type: String choice

Formats: - markdown - Human-readable Markdown - json - Structured JSON data - csv - Spreadsheet format

Examples¶

Example 1: Markdown Export

lixplore --export-annotations markdown

Creates: lixplore_annotations_TIMESTAMP.md

Example 2: JSON Export

lixplore --export-annotations json

Creates: lixplore_annotations_TIMESTAMP.json

Example 3: CSV Export

lixplore --export-annotations csv

Creates: lixplore_annotations_TIMESTAMP.csv

`--annotation-stats`¶

Description: Show annotation statistics.

Syntax:

lixplore --annotation-stats

Type: Boolean flag

Statistics Shown: - Total annotated articles - Rating distribution - Read status breakdown - Priority distribution - Comment count - Unique tags count

Examples¶

Example 1: View Statistics

lixplore --annotation-stats

Output:

ANNOTATION STATISTICS
Total Annotated Articles: 42

Rating Distribution:
  ⭐⭐⭐⭐⭐ (5): ████████ 8
  ⭐⭐⭐⭐ (4): ████████████ 12
  ⭐⭐⭐ (3): ██████ 6

Read Status:
  Read: 25
  Reading: 10
  Unread: 7

Priority:
  High: 15
  Medium: 20
  Low: 7

Tags: 67 unique tags

`--delete-annotation`¶

Description: Delete annotation for specific article.

Syntax:

lixplore --delete-annotation N

Type: Integer (article number from last search)

Examples¶

Example 1: Delete Annotation

# Search first
lixplore -P -q "cancer" -m 20

# Delete annotation for article #5
lixplore --delete-annotation 5

Annotation Workflows¶

Workflow 1: Paper Review¶

# 1. Search for papers
lixplore -P -q "machine learning healthcare" -m 30 -a

# 2. Initial screening (rate based on abstracts)
lixplore --annotate 3 --rating 5 --tags "relevant,must-read" --priority high
lixplore --annotate 7 --rating 4 --tags "relevant" --priority medium
lixplore --annotate 12 --rating 2 --tags "not-relevant" --priority low

# 3. Mark for reading
lixplore --annotate 3 --read-status reading

# 4. After reading, add detailed notes
lixplore --annotate 3 \
  --comment "Excellent RCT design. N=500, p<0.001. Key for my methodology chapter." \
  --tags "relevant,must-cite,methodology,chapter2" \
  --read-status read

# 5. View high-priority unread papers
lixplore --filter-annotations "priority=high,read_status=unread"

Workflow 2: Literature Review¶

# 1. Comprehensive search
lixplore -A -q "cancer immunotherapy" -m 200 -D --sort newest

# 2. Quick screening - mark important ones
lixplore --annotate 1 --rating 5 --priority high
lixplore --annotate 5 --rating 5 --priority high
lixplore --annotate 8 --rating 4 --priority medium

# 3. Add topical tags
lixplore --annotate 1 --tags "checkpoint-inhibitors,melanoma"
lixplore --annotate 5 --tags "CAR-T,leukemia"

# 4. Export must-cite papers
lixplore --filter-annotations "min_rating=5"
lixplore --export-annotations markdown

Workflow 3: Reading List Management¶

# 1. Find papers and create reading list
lixplore -P -q "systematic review methodology" -m 50 --sort newest
lixplore --annotate 1 --read-status unread --priority high --tags "learn,methodology"
lixplore --annotate 3 --read-status unread --priority high --tags "learn,methodology"
lixplore --annotate 5 --read-status unread --priority medium --tags "reference"

# 2. Start reading
lixplore --filter-annotations "read_status=unread,priority=high"
lixplore --annotate 1 --read-status reading

# 3. Complete reading and annotate
lixplore --annotate 1 \
  --read-status read \
  --rating 5 \
  --comment "Best guide on systematic reviews. Reference for methods section."

# 4. Check progress
lixplore --annotation-stats

Workflow 4: Organization by Project¶

# Tag by dissertation chapter
lixplore --annotate 1 --tags "chapter1,introduction,background"
lixplore --annotate 5 --tags "chapter2,methodology,statistics"
lixplore --annotate 10 --tags "chapter3,results,analysis"
lixplore --annotate 15 --tags "chapter4,discussion,implications"

# Find all chapter 2 papers
lixplore --search-annotations "chapter2"
lixplore --filter-annotations "tag=methodology"

# Export chapter-specific bibliography
lixplore --search-annotations "chapter2"
lixplore --export-annotations markdown

Best Practices¶

1. Consistent Tagging System¶

Create Tag Vocabulary: - Topics: methodology, results, review, meta-analysis - Quality: excellent, good, fair, poor - Action: read-later, cite, discuss, follow-up - Project: chapter1, chapter2, intro, discussion

2. Rate Immediately After Reading¶

# Don't wait - annotate while fresh
lixplore --annotate 5 \
  --rating 5 \
  --read-status read \
  --comment "Detailed notes here..." \
  --tags "relevant,cite"

3. Use Priority for Time Management¶

# High priority = read this week
lixplore --annotate 1 --priority high --read-status unread

# Medium = read this month
lixplore --annotate 5 --priority medium --read-status unread

# Low = read if time permits
lixplore --annotate 10 --priority low --read-status unread

4. Regular Exports for Backup¶

# Weekly backup
lixplore --export-annotations json
lixplore --export-annotations markdown

5. Review Statistics Periodically¶

# Monthly check-in
lixplore --annotation-stats
lixplore --filter-annotations "read_status=unread,priority=high"

Tips & Tricks¶

Quick Rating Scale¶

5 stars: Foundational paper, must cite
4 stars: Very relevant, high quality
3 stars: Useful reference, good to have
2 stars: Tangentially relevant
1 star: Not useful / poor quality

Effective Commenting¶

Good Comments: - "RCT, N=500, primary outcome p<0.001, relevant for methods" - "Cite in intro for background on X" - "Methodology section: novel approach to Y"

Avoid: - "Good paper" (not specific) - "Read this" (use priority/read-status instead)

Tag Organization¶

Use Hierarchical Tags: - topic-subtopic: e.g., ML-neural-networks, stats-regression - project-chapter: e.g., diss-chapter2, paper1-methods

Last Updated: 2024-12-28

Annotation System Flags¶

Table of Contents¶

Overview¶

Creating Annotations¶

--annotate¶

Examples¶

--comment¶

Examples¶

--rating¶

Examples¶

--tags¶

Examples¶

--read-status¶

Examples¶

--priority¶

Examples¶

Viewing Annotations¶

--show-annotation¶

Examples¶

--list-annotations¶

Examples¶

--filter-annotations¶

Examples¶

--search-annotations¶

Examples¶

Managing Annotations¶

--export-annotations¶

Examples¶

--annotation-stats¶

Examples¶

--delete-annotation¶

Examples¶

Annotation Workflows¶

Workflow 1: Paper Review¶

Workflow 2: Literature Review¶

Workflow 3: Reading List Management¶

Workflow 4: Organization by Project¶

Best Practices¶

1. Consistent Tagging System¶

2. Rate Immediately After Reading¶

3. Use Priority for Time Management¶

4. Regular Exports for Backup¶

5. Review Statistics Periodically¶

Tips & Tricks¶

Quick Rating Scale¶

Effective Commenting¶

Tag Organization¶

`--annotate`¶

`--comment`¶

`--rating`¶

`--tags`¶

`--read-status`¶

`--priority`¶

`--show-annotation`¶

`--list-annotations`¶

`--filter-annotations`¶

`--search-annotations`¶

`--export-annotations`¶

`--annotation-stats`¶

`--delete-annotation`¶