biorxiv-database

Name: biorxiv-database
Author: LeonChaoX

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How to install biorxiv-database?

leonchaox/qinyan-academic-skills/biorxiv-database

$npx -y skills add LeonChaoX/qinyan-academic-skills --skill biorxiv-database

Installs into the current project.

Summary

Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.

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SKILL.md

1	# bioRxiv Database
2
3	## Overview
4
5	This skill provides efficient Python-based tools for searching and retrieving preprints from the bioRxiv database. It enables comprehensive searches by keywords, authors, date ranges, and categories, returning structured JSON metadata that includes titles, abstracts, DOIs, and citation information. The skill also supports PDF downloads for full-text analysis.
6
7	## When to Use This Skill
8
9	Use this skill when:
10	- Searching for recent preprints in specific research areas
11	- Tracking publications by particular authors
12	- Conducting systematic literature reviews
13	- Analyzing research trends over time periods
14	- Retrieving metadata for citation management
15	- Downloading preprint PDFs for analysis
16	- Filtering papers by bioRxiv subject categories
17
18	## Core Search Capabilities
19
20	### 1. Keyword Search
21
22	Search for preprints containing specific keywords in titles, abstracts, or author lists.
23
24	Basic Usage:
25	```python
26	python scripts/biorxiv_search.py \
27	--keywords "CRISPR" "gene editing" \
28	--start-date 2024-01-01 \
29	--end-date 2024-12-31 \
30	--output results.json
31	```
32
33	With Category Filter:
34	```python
35	python scripts/biorxiv_search.py \
36	--keywords "neural networks" "deep learning" \
37	--days-back 180 \
38	--category neuroscience \
39	--output recent_neuroscience.json
40	```
41
42	Search Fields:
43	By default, keywords are searched in both title and abstract. Customize with `--search-fields`:
44	```python
45	python scripts/biorxiv_search.py \
46	--keywords "AlphaFold" \
47	--search-fields title \
48	--days-back 365
49	```
50
51	### 2. Author Search
52
53	Find all papers by a specific author within a date range.
54
55	Basic Usage:
56	```python
57	python scripts/biorxiv_search.py \
58	--author "Smith" \
59	--start-date 2023-01-01 \
60	--end-date 2024-12-31 \
61	--output smith_papers.json
62	```
63
64	Recent Publications:
65	```python
66	# Last year by default if no dates specified
67	python scripts/biorxiv_search.py \
68	--author "Johnson" \
69	--output johnson_recent.json
70	```
71
72	### 3. Date Range Search
73
74	Retrieve all preprints posted within a specific date range.
75
76	Basic Usage:
77	```python
78	python scripts/biorxiv_search.py \
79	--start-date 2024-01-01 \
80	--end-date 2024-01-31 \
81	--output january_2024.json
82	```
83
84	With Category Filter:
85	```python
86	python scripts/biorxiv_search.py \
87	--start-date 2024-06-01 \
88	--end-date 2024-06-30 \
89	--category genomics \
90	--output genomics_june.json
91	```
92
93	Days Back Shortcut:
94	```python
95	# Last 30 days
96	python scripts/biorxiv_search.py \
97	--days-back 30 \
98	--output last_month.json
99	```
100
101	### 4. Paper Details by DOI
102
103	Retrieve detailed metadata for a specific preprint.
104
105	Basic Usage:
106	```python
107	python scripts/biorxiv_search.py \
108	--doi "10.1101/2024.01.15.123456" \
109	--output paper_details.json
110	```
111
112	Full DOI URLs Accepted:
113	```python
114	python scripts/biorxiv_search.py \
115	--doi "https://doi.org/10.1101/2024.01.15.123456"
116	```
117
118	### 5. PDF Downloads
119
120	Download the full-text PDF of any preprint.
121
122	Basic Usage:
123	```python
124	python scripts/biorxiv_search.py \
125	--doi "10.1101/2024.01.15.123456" \
126	--download-pdf paper.pdf
127	```
128
129	Batch Processing:
130	For multiple PDFs, extract DOIs from a search result JSON and download each paper:
131	```python
132	import json
133	from biorxiv_search import BioRxivSearcher
134
135	# Load search results
136	with open('results.json') as f:
137	data = json.load(f)
138
139	searcher = BioRxivSearcher(verbose=True)
140
141	# Download each paper
142	for i, paper in enumerate(data['results'][:10]): # First 10 papers
143	doi = paper['doi']
144	searcher.download_pdf(doi, f"papers/paper_{i+1}.pdf")
145	```
146
147	## Valid Categories
148
149	Filter searches by bioRxiv subject categories:
150
151	- `animal-behavior-and-cognition`
152	- `biochemistry`
153	- `bioengineering`
154	- `bioinformatics`
155	- `biophysics`
156	- `cancer-biology`
157	- `cell-biology`
158	- `clinical-trials`
159	- `developmental-biology`
160	- `ecology`
161	- `epidemiology`
162	- `evolutionary-biology`
163	- `genetics`
164	- `genomics`
165	- `immunology`
166	- `microbiology`
167	- `molecular-biology`
168	- `neuroscience`
169	- `paleontology`
170	- `pathology`
171	- `pharmacology-and-toxicology`
172	- `physiology`
173	- `plant-biology`
174	- `scientific-communication-and-education`
175	- `synthetic-biology`
176	- `systems-biology`
177	- `zoology`
178
179	## Output Format
180
181	All searches return structured JSON with the following format:
182
183	```json
184	{
185	"query": {
186	"keywords": ["CRISPR"],
187	"start_date": "2024-01-01",
188	"end_date": "2024-12-31",
189	"category": "genomics"
190	},
191	"result_count": 42,
192	"results": [
193	{
194	"doi": "10.1101/2024.01.15.123456",
195	"title": "Paper Title Here",
196	"authors": "Smith J, Doe J, Johnson A",
197	"author_corresponding": "Smith J",
198	"author_corresponding_institution": "University Example",
199	"da

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biorxiv-database

698stars61forks

View on GitHub

How to install biorxiv-database?

leonchaox/qinyan-academic-skills/biorxiv-database

$npx -y skills add LeonChaoX/qinyan-academic-skills --skill biorxiv-database

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# bioRxiv Database
2
3	## Overview
4
5	This skill provides efficient Python-based tools for searching and retrieving preprints from the bioRxiv database. It enables comprehensive searches by keywords, authors, date ranges, and categories, returning structured JSON metadata that includes titles, abstracts, DOIs, and citation information. The skill also supports PDF downloads for full-text analysis.
6
7	## When to Use This Skill
8
9	Use this skill when:
10	- Searching for recent preprints in specific research areas
11	- Tracking publications by particular authors
12	- Conducting systematic literature reviews
13	- Analyzing research trends over time periods
14	- Retrieving metadata for citation management
15	- Downloading preprint PDFs for analysis
16	- Filtering papers by bioRxiv subject categories
17
18	## Core Search Capabilities
19
20	### 1. Keyword Search
21
22	Search for preprints containing specific keywords in titles, abstracts, or author lists.
23
24	Basic Usage:
25	```python
26	python scripts/biorxiv_search.py \
27	--keywords "CRISPR" "gene editing" \
28	--start-date 2024-01-01 \
29	--end-date 2024-12-31 \
30	--output results.json
31	```
32
33	With Category Filter:
34	```python
35	python scripts/biorxiv_search.py \
36	--keywords "neural networks" "deep learning" \
37	--days-back 180 \
38	--category neuroscience \
39	--output recent_neuroscience.json
40	```
41
42	Search Fields:
43	By default, keywords are searched in both title and abstract. Customize with `--search-fields`:
44	```python
45	python scripts/biorxiv_search.py \
46	--keywords "AlphaFold" \
47	--search-fields title \
48	--days-back 365
49	```
50
51	### 2. Author Search
52
53	Find all papers by a specific author within a date range.
54
55	Basic Usage:
56	```python
57	python scripts/biorxiv_search.py \
58	--author "Smith" \
59	--start-date 2023-01-01 \
60	--end-date 2024-12-31 \
61	--output smith_papers.json
62	```
63
64	Recent Publications:
65	```python
66	# Last year by default if no dates specified
67	python scripts/biorxiv_search.py \
68	--author "Johnson" \
69	--output johnson_recent.json
70	```
71
72	### 3. Date Range Search
73
74	Retrieve all preprints posted within a specific date range.
75
76	Basic Usage:
77	```python
78	python scripts/biorxiv_search.py \
79	--start-date 2024-01-01 \
80	--end-date 2024-01-31 \
81	--output january_2024.json
82	```
83
84	With Category Filter:
85	```python
86	python scripts/biorxiv_search.py \
87	--start-date 2024-06-01 \
88	--end-date 2024-06-30 \
89	--category genomics \
90	--output genomics_june.json
91	```
92
93	Days Back Shortcut:
94	```python
95	# Last 30 days
96	python scripts/biorxiv_search.py \
97	--days-back 30 \
98	--output last_month.json
99	```
100
101	### 4. Paper Details by DOI
102
103	Retrieve detailed metadata for a specific preprint.
104
105	Basic Usage:
106	```python
107	python scripts/biorxiv_search.py \
108	--doi "10.1101/2024.01.15.123456" \
109	--output paper_details.json
110	```
111
112	Full DOI URLs Accepted:
113	```python
114	python scripts/biorxiv_search.py \
115	--doi "https://doi.org/10.1101/2024.01.15.123456"
116	```
117
118	### 5. PDF Downloads
119
120	Download the full-text PDF of any preprint.
121
122	Basic Usage:
123	```python
124	python scripts/biorxiv_search.py \
125	--doi "10.1101/2024.01.15.123456" \
126	--download-pdf paper.pdf
127	```
128
129	Batch Processing:
130	For multiple PDFs, extract DOIs from a search result JSON and download each paper:
131	```python
132	import json
133	from biorxiv_search import BioRxivSearcher
134
135	# Load search results
136	with open('results.json') as f:
137	data = json.load(f)
138
139	searcher = BioRxivSearcher(verbose=True)
140
141	# Download each paper
142	for i, paper in enumerate(data['results'][:10]): # First 10 papers
143	doi = paper['doi']
144	searcher.download_pdf(doi, f"papers/paper_{i+1}.pdf")
145	```
146
147	## Valid Categories
148
149	Filter searches by bioRxiv subject categories:
150
151	- `animal-behavior-and-cognition`
152	- `biochemistry`
153	- `bioengineering`
154	- `bioinformatics`
155	- `biophysics`
156	- `cancer-biology`
157	- `cell-biology`
158	- `clinical-trials`
159	- `developmental-biology`
160	- `ecology`
161	- `epidemiology`
162	- `evolutionary-biology`
163	- `genetics`
164	- `genomics`
165	- `immunology`
166	- `microbiology`
167	- `molecular-biology`
168	- `neuroscience`
169	- `paleontology`
170	- `pathology`
171	- `pharmacology-and-toxicology`
172	- `physiology`
173	- `plant-biology`
174	- `scientific-communication-and-education`
175	- `synthetic-biology`
176	- `systems-biology`
177	- `zoology`
178
179	## Output Format
180
181	All searches return structured JSON with the following format:
182
183	```json
184	{
185	"query": {
186	"keywords": ["CRISPR"],
187	"start_date": "2024-01-01",
188	"end_date": "2024-12-31",
189	"category": "genomics"
190	},
191	"result_count": 42,
192	"results": [
193	{
194	"doi": "10.1101/2024.01.15.123456",
195	"title": "Paper Title Here",
196	"authors": "Smith J, Doe J, Johnson A",
197	"author_corresponding": "Smith J",
198	"author_corresponding_institution": "University Example",
199	"da

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