old_review-neuro-meta-analyses#
You can see the full contents of this project on GitHub.
Papers#
How the papers were obtained [to be updated]#
There are two groups of papers:
full-text open-access papers that were obtained from PMC via pubget, and
abstracts from closed-access papers that were obtained from PubMed via a tweaked version of pubget (the out-of-the-box version can only access PMC).
Typically with pubget.
We recommend invoking pubget
with the --query_file
option, and storing a copy of the query file in the project’s directory, or including a copy in the README.md
.
<description>
Where the full papers are stored [to be updated]#
Typically on OSF.
Please also add a documents/datasets.json
file containing the URL where the full pubget
dataset can be downloaded, that looks like:
[ { "url": "https://osf.io/download/<...>/" } ]
<description>
Annotations#
File(s) being annotated:#
full texts from open-access papers from PMC:
/projects/review-neuro-meta-analayses/documents/documents_00001-ma-in-title.jsonl
/projects/review-neuro-meta-analayses/documents/documents_00002-ma-in-title.jsonl
/projects/review-neuro-meta-analayses/documents/documents_00003-ma-in-title.jsonl
abstracts from closed-access papers from pubmed:
projects/review-neuro-meta-analyses/documents/closed_documents_00000.jsonl
Annotation labels:#
The label list is quite long, so I’m not including it here. But the labels group into these categories
Reasons to come back to the paper
info on the number of studies/contrasts found/included
meta-analysis number (many papers have multiple)
algorithm
software
large-scale meta-analysis method
exclusion criteria
has prisma chart
Labels found in other projects as well:#
<label2>
Instructions for annotators#
At this point, I have finished annotating the open-access full-text papers. I’d love help annotating the closed-access abstracts. To do this, follow these steps:
install labelbuddy
install labelbudd-annotations
navigate to the current directory
projects/review-neuro-meta-analyses
start labelbuddy with this code:
labelbuddy review-neuro-meta-analyses.lb
import the documents
projects/review-neuro-meta-analyses/documents/closed_documents_00000.jsonl
import the labels
projects/review-neuro-meta-analyses/labels/labels.jsonl
impport my annotations so you don’t work on papers I’ve already finished
projects/review-neuro-meta-analyses/annotations/Kendra_Oudyk.jsonl
Once you’re done annotating, export your annotations (without including the document text) to a file called
projects/review-neuro-meta-analyses/annotations/<Firstname_Lastname>.jsonl
add, commit, and push your annotations to this repo
Labels in this project#
N studies included (598 docs)
Example annotations:
DONE (but did not look into full paper) (529 docs)
Example annotations:
algorithm-ALE (428 docs)
Example annotations:
software-gingerale (222 docs)
Example annotations:
MA1 (200 docs)
Example annotations:
DONE (194 docs)
Example annotations:
MA2 (159 docs)
Example annotations:
N contrasts included (111 docs)
Example annotations:
exclude (109 docs)
Example annotations:
N studies found (102 docs)
Example annotations:
MA3 (99 docs)
Example annotations:
algorithm-SDM (80 docs)
Example annotations:
EXCLUDE - traditional ma (57 docs)
Example annotations:
MA4 (52 docs)
Example annotations:
thresholding (48 docs)
Example annotations:
largescale-MACM (45 docs)
Example annotations:
has prisma chart (44 docs)
Example annotations:
EXCLUDE - about ma's (34 docs)
Example annotations:
read later (33 docs)
Example annotations:
NO N studies found (30 docs)
Example annotations:
ask about this one (29 docs)
Example annotations:
algorithm-MKDA (28 docs)
Example annotations:
algorithm-AES-SDM (28 docs)
Example annotations:
MA5 (25 docs)
Example annotations:
EXCLUDE - not a full report (22 docs)
Example annotations:
software-none-or-unclear (21 docs)
Example annotations:
algorithm-other ma method (20 docs)
Example annotations:
algorithm-SDM-PSI (18 docs)
Example annotations:
MA6 (17 docs)
Example annotations:
largescale-neurosynth decoding (16 docs)
Example annotations:
algorithm-ES-SDM (14 docs)
Example annotations:
software-brainmap (11 docs)
Example annotations:
largescale-brainmap decoding (11 docs)
Example annotations:
NO N studies included (10 docs)
Example annotations:
MA7 (10 docs)
Example annotations:
candidate for replication (9 docs)
Example annotations:
IMBA (9 docs)
Example annotations:
largescale-neurosynth encoding (9 docs)
Example annotations:
EXCLUDE - protocol (9 docs)
Example annotations:
MA8 (8 docs)
Example annotations:
software-other (8 docs)
Example annotations:
EXCLUDE - review (8 docs)
Example annotations:
software-MKDA toolbox (7 docs)
Example annotations:
N group-level stat maps included (6 docs)
Example annotations:
software-spm (6 docs)
Example annotations:
MA9 (5 docs)
Example annotations:
stopped here (4 docs)
Example annotations:
MA10 (4 docs)
Example annotations:
MA12 (4 docs)
Example annotations:
label-based review/MA (4 docs)
Example annotations:
N MAs (3 docs)
Example annotations:
MA11 (3 docs)
Example annotations:
MA13 (3 docs)
Example annotations:
software-neuroelf (3 docs)
Example annotations:
no-access (2 docs)
Example annotations:
software-CluB (2 docs)
Example annotations:
software-canlab mkda (2 docs)
Example annotations:
software-nimare (2 docs)
Example annotations:
MA14 (1 docs)
Example annotations:
algorithm-ABC (1 docs)
Example annotations:
algorithm-KDA (1 docs)
Example annotations:
software-abc (1 docs)
Example annotations:
largescale-neurosynth MACM (1 docs)
Example annotations:
largescale-neuroquery encoding (1 docs)
Example annotations:
largescale-other-or-undefined (1 docs)
Example annotations:
EXCLUDE - previous ma for seed / roi (1 docs)
Example annotations:
EXCLUDE - not about the brain (1 docs)
Example annotations:
EXCLUDE - non-human focus (1 docs)
Example annotations:
NO N contrasts included (0 docs)
(No annotations with this label in the current project)
EXCLUDE - cites ma as justification (0 docs)
(No annotations with this label in the current project)
EXCLUDE - cites ma as consistent with findings (0 docs)
(No annotations with this label in the current project)
EXCLUDE - preprint (0 docs)
(No annotations with this label in the current project)
EXCLUDE - not a ma, doesn't fit other exclusion (0 docs)
(No annotations with this label in the current project)
EXCLUDE - ma not in title (0 docs)
(No annotations with this label in the current project)