Archive for the ‘Inside NIF’ Category

Top 25 for April

Posted on April 14th, 2013 in Inside NIF, News & Events | No Comments »

Its that time, we find out what have the users of NIF been searching for this month.
Looks like antibodies and money are still winners, but some interesting things climbing to the top. The gene ontology tools, which has joined the NIF registry is now in the top 10 search terms and the BAMS connectivity data seem to be a big winner this month.

Top databases of April are:
2. ABCD/Brain Regions
3. BAMSCN/Con1
4. AllenInstitute/MouseBrainAtlas
5. BioNOT/Negation
6. AntibodyRegistry/ABs
7. NIF Integrated NSC/Connectivity
8. AmiGO/Genes
9. AddGene/Plasmids
10. BAMS/Brain Regions
11. NINDS/Disease 1
12. BrainInfo/Brain Region
13. Drug Related Gene Database/DRG
14. BREDE/Activation Foci
15. BrainMaps/Atlas
16. NIF Registry/Info
17. ClinicalTrials/ClinTr
18. CGC/Animals 3
19. CellImageLibrary/CIL
20. RePORTER/CurrentNIHGrants
21. ModelDB/Models
22. NIF Integrated Software/Info
23. SumsDB/Activation Foci
24. Allenbrain/Atlas

Top Search Terms of April:
1. antibodies
2. cerebellum
3. database
4. hippocampus
5. “Forebrain”
6. “Gene Ontology Tools”
7. “Frontal Lobe”
8. antibodyregistry
9. “Anterior Nuclear Group”
10. “Cerebellum”
11. NIDA
12. “Amygdala”
13. “Drug Related Gene Database”
14. “Hypothalamus”
15. “cerebellum”
16. “Flocculonodular Lobe”
17. brain
18. parkinson disease
19. parkinson’s disease
20. “Basal Ganglia”
21. “Medium Spiny Neuron”
22. “NIF Integrated Software”
23. “Oligodendrocyte Precursor Cell”
24. mouse development atlas
25. “Brainstem”

Nature seeing a trend?

Posted on March 31st, 2013 in Anita Bandrowski, Force11, Inside NIF, News & Events | No Comments »

Although the pace of science often seems glacial, returning from the Beyond the PDF2 meeting, I have been struck at how much scientific publishing has changed in the last 18 months, since the first beyond the pdf meeting.

Not many scientific meetings really are transformative, so this one has been a rare gem in the great sea of ‘same old’. It seems that major publishers (most present at the meeting), have also started to pay attention.

This week Nature has used its influence to comment on this very issue in the form of various editorials.

They address open access to the scientific literature, which was a big topic of conversation at the last beyond the pdf, a topic conspicuously absent this time. Open access is here, we need to still work out some kinks, as Nature is pointing out, but essentially it is solved. Ok, perhaps not solved, especially if you are talking about access by machines (e.g., statistical algorithms) and publication costs are still too high for the humanities and those in the third world, but as a topic of conversation as to whether we should have access, the jury is in and implementation awaits. So now that anyone will have access to an increasing quantity of the world’s publications, what now?

My read of the next steps are largely what the meeting kept oscillating between: data vs prose. The data side seems to believe that if we can have data as a publication because prose is a highly imperfect way of communicating about data. We could now have access to everyone’s raw data and then all will be well? The other side (including the advocacy for the pen and paper) also has an interesting point, it turns out that the human species has evolved to communicate by using language, not statistical inference.

My analysis of this meeting is: Yes you will have access to the scientific literature, but the problem of data is far from solved, in fact the problem of data is only now starting to be considered. I do not sit on the sidelines of this discussion, at NIF we have data, compare data from different sources, but even so, I wonder if the lack of prose will be as great a problem as all prose.

Top 25 for March

Posted on March 15th, 2013 in Force11, Inside NIF, News & Events | No Comments »

Top 25 Databases:
2. AntibodyRegistry/ABs
3. BioNOT/Negation
4. ABCD/Brain Regions
5. AmiGO/Genes
7. BioGRID/Interactions
8. NIF Registry/Info
9. AddGene/Plasmids
10. BrainMaps/Atlas
11. ClinicalTrials/ClinTr
12. NIF Integrated Disease/Info
13. BAMS/Brain Regions
14. BrainInfo/Brain Region
15. AllenInstitute/MouseBrainAtlas
16. RePORTER/CurrentNIHGrants
17. Allenbrain/Atlas
18. HumanBrainAtlas/Michigan
19. CellImageLibrary/CIL
20. ModelDB/Models
21. OMIM/Genes
22. BREDE/Activation Foci
23. ResearchCrossroads/Grants
24. SumsDB/Activation Foci
25. NIF Integrated CT/Registry

Top 25 Search terms:
1. antibodyregistry
2. database
3. “Anterior Nuclear Group”
4. “Drug Related Gene Database”
5. “Forebrain”
6. Brodmann area 44
7. “Cerebellum”
8. “Gene Ontology Tools”
9. cerebellum
10. hippocampus
11. “Fusiform Gyrus”
12. “Mitral Cell”
13. “Oligodendrocyte Precursor Cell”
14. “Brainstem”
15. “Flocculonodular Lobe”
16. “Fornix”
17. “Frontal Lobe”
18. “Hypothalamus”
19. “Medium Spiny Neuron”
20. “Basal Ganglia”
21. “Photoreceptor Cell”
22. gene
22. “Amygdala”
23. “Cerebral Crus”
24. “Cerebrum”
25. “Motor Neuron”

How to define an Action Potential?

Posted on February 26th, 2013 in Anita Bandrowski, Force11, Inside NIF, News & Events, NIFarious Ideas | No Comments »

Dear electrophysiologists,

If you could spare about 5 minutes of your time, the INCF electrophysiology task force is attempting to survey the landscape of definitions of the action potential. The main interest here is to determine how working physiologists view it, is it an event, property of the membrane or a process?

The following link will take you to a google-survey, click here or follow this link:

The results will be stored on a google spreadsheet and the answers will be used to design a relevant knowledge model to describe electrophysiology data with the Experimental Neurophysiology Ontology (ENO).

Thank you in advance for any help you can provide.

Top 25 for February

Posted on February 15th, 2013 in Data Spotlight, Inside NIF | No Comments »

Top 25 Databases of the month, show that once again people are mostly looking for funding, but antibodies are a close second. This month it looks like several sources of brain region information including 4 atlases are on top.

2 AntibodyRegistry/ABs
3 BioNOT/Negation
4 ABCD/Brain Regions
5 AmiGO/Genes
6 NIF Registry/Info
7 AllenInstitute/MouseBrainAtlas
8 BAMS/Brain Regions
9 ClinicalTrials/ClinTr
10 RePORTER/CurrentNIHGrants
11 AddGene/Plasmids
12 NIF Annotation/Info
13 BrainInfo/Brain Region
14 BrainMaps/Atlas
15 Allenbrain/Atlas
16 OMIM/Genes
17 Drug Related Gene Database/DRG
18 ModelDB/Models
19 HumanBrainAtlas/Michigan
20 BREDE/Activation Foci
21 NIF Integrated Nervous System/Connectivity
22 ResearchCrossroads/Grants
23 bioDBcore/Databases
24 GEO/Gene Expression Omnibus
25 NIF Integrated Disease/Info

Top 25 search terms
1 antibodyregistry
2 Database OR “Database resource” OR Databases OR “Data base”
3 Cerebellum
4 “Gene Ontology Tools”
5 “Drug Related Gene Database”
6 Hippocampus OR “ammon horn” OR “Ammon’s horn” OR “Cornu ammonis” OR “hippocampus proper”
7 Brain OR Br
8 “Cerebellar Purkinje neuron” OR “Purkinje Cell” OR “Purkinje neuron” OR “Purkinje’s corpuscles”
9 Amygdala OR “amygdaloid nucleus” OR “amygdaloid body” OR “Amygdaloid complex” OR archistriatum
10 Brainstem OR “brain stem”
11 “Frontal lobe”
12 “Traumatic brain injury” OR “intracranial injury” OR TBI
13 Neuron OR “neuron cell” OR “nerve cell”
14 “Cerebral cortex” OR Cortex
15 Epithalamus OR ETh
16 Habenula OR Hb OR “habenular nucleus”
17 Grammatical_encoding
18 “Anterior nuclear group” OR “anterior thalamus” OR ANG OR “nuclei anterior thalami”
19 Zebrafish OR Rerio OR “Perilampus striatus” OR “Danio rerio” OR “Cyprinus rerio” OR “Cyprinus chapalio”
20 “Locus coeruleus NA neuron” OR “Locus coeruleus noradrenergic neuron”
21 “Olfactory bulb \main\ mitral cell” OR “Olfactory bulb main mitral cell” OR MC OR “Mitral neuron” OR “Mitral cell”
22 Parkinsons OR “Parkinson disease” OR “Parkinson syndrome” OR “Paralysis Agitans” OR “Idiopathic PD”
23 “Retinal Cone Cell” OR “retinal core” OR “Cone cell” OR cone
24 Diencephalon OR DiE OR Interbrain
25 “Gyrus rectus”

A game for neuroscientists?

Posted on November 27th, 2012 in Force11, Inside NIF, News & Events | 1 Comment »

The Society for Neuroscience meeting has come and gone and among my personal highlights was the Neuroinformatics social (the cell death social came in as a close second, but only because of the name). This year, the organizer David Kennedy asked various people to give brief talks about their resources, but rather than the usual presentation, and, as this was a social,  NIF decided to run a game based on our new analytics.   We called this game:  Does anything ever not require further study?

If you want to play, don’t scroll to the bottom until you have tried to answer this question:

What terms go down in frequency over time in the biomedical literature?

Now, you must know that the cards are stacked in the favor of the house because we are publishing an ever increasing amount of papers per year, over 1M in 2011.   When we were testing the tool, almost every query resulted in increased mentions over time,  so finding a term that is decreasing in prevalence is actually not as easy as you may think.

Here is how you can play:
Go to the literature section of the new NIF interface (still beta) and then click on the Graph button (then chose the graph by year option).  This tool plots the frequency of the search term over time in articles available through Pub Med.  *Note, the last two points don’t count because those are the current year (2012) and the next year (2013).

We thought that some of the veteran neuroscientists would win because they would know of some obscure brain regions that are no longer studied, but although these sage scientists were given multiple chances they apparently know no terms from the 1960′s that are less popular now.

The winner was Shreejoy Tripathy, a young researcher who has spent a significant portion of his professional life text-mining the biomedical literature and may have had a-priori knowledge. His winning term was HRP, an intracellular tracer that was very popular in the 1980′s.  We were not sure whether he should be disqualified, but Christian Haselgrove probably had the most original answer: lobotomy!

Top 25 Accessed Databases at NIF from Sept. 4 – Oct. 4, 2012

Posted on October 5th, 2012 in General information, Inside NIF, News & Events | No Comments »

Here are the top 25 Accessed Databases at NIF from Sept. 4 – Oct. 4, 2012.

2.  AntibodyRegistry/ABs
3.  BioNOT/Negation
4.  ABCD/Brain Regions
5.  AllenInstitute/MouseBrainAtlas
6.  AmiGO/Genes
7.  NIF Integrated Nervous System/Connectivity
8.  BAMS/Brain Regions
9.  NIF Registry/info
10. NIF Registry/Info
11. OneMind/BioBanks
12. BrainMaps/Atlas
13. ClinicalTrials/ClinTr
14. NIF Integrated Software/Info
15. NIF Integrated Animals/Available
16. NIF Annotation/Info
17. Drug Related Gene Database/DRG
18. AddGene/Plasmids
19. bioDBcore/Databases
20. RePORTER/CurrentNIHGrants
21. WikiPathways/ChemPathway
22. BioGRID/Interactions
23. BrainInfo/Brain Region
24. Gemma/Microarray
25. OMIM/Genes

Top 25 Search Terms at NIF from Sept. 4 – Oct. 4, 2012

Posted on October 5th, 2012 in General information, Inside NIF, News & Events, Uncategorized | No Comments »

Here are the top 25 Search Terms at NIF from Sept. 4 – Oct. 4, 2012.

1.  antibodyregistry
2.  database
3.  “DOMMINO – Database Of MacroMolecular INteractiOns”
4.  “Rhode Island Biobank”
5.  “Frontal Lobe”
6.  “Purkinje Cell”
7.  “Satellite Cell”
8.  hippocampus
9.  “Diencephalon”
10.  “Drug Related Gene Database”
11.  cerebellum
12.  “ALSA – The Australian Longitudinal Study of Ageing”
13.  “Amygdala”
14.  “Angular Gyrus”
15.  “Brainstem”
16.  “Cerebellum”
17.  “Forebrain”
18.  “Hypothalamus”
19.  “Mitral Cell”
20.  “Astrocyte”
21.  “Cingulate Cortex”
22.  “Cone Cell”
23.  “Hippocampus”
24.  “Medium Spiny Neuron”
25.  “Anterior Nucleus of the hypthalamus”

Frontiers in Addiction Research Mini-convention – Oct 12, 2012, New Orleans, LA

Posted on September 21st, 2012 in General information, Inside NIF, News & Events | No Comments »

Frontiers in Addiction Research Mini-convention
Sponsored by the National Institute on Drug Abuse

Friday, October 12, 2012

Sheraton New Orleans Hotel, 500 Canal Street, New Orleans, LA

Seating is limited.  Additional information and registration can be found at:

The NIDA mini-convention, Frontiers in Addiction Research, held in conjunction with the annual Society for Neuroscience Meeting, will feature outstanding scientists who will present their cutting-edge research on the neurobiology of drug abuse and addiction.  The NIDA mini-convention features four symposia, the SfN Jacob P. Waletzky Memorial Lecture and a poster session for early career investigators.  The agenda this year includes:

8:00 am- 8:15 am                  Welcome: NIDA Director

8:15 am- 9:35 am                   Ghrelin, Leptin and Insulin Modulates Reward

9:35 am-10:10 am                 Jacob P. Waletzky Memorial Lecture

10:35 am-12:15 pm                 Role of Phagocytes in Synaptic Plasticity & Remodeling in the Nervous System

12:15 pm- 2:15 pm                  Early Career Investigators Poster Session

2:15 pm- 3:35 pm                  Brain Energetics and Neurotransmission: Fueling Neurons and Glia

3:50 pm-5:25 pm                   Central Nervous System Immune Signaling and Addiction

NIDA will also hold several other events at the Society for Neuroscience meeting, including:

1)      Toni S. Shippenberg Memorial Symposium – Friday, October 12, 2012, 6:00-7:30 p.m.

2)      Julius Axelrod Lecture and Poster Session – Sunday, October 14, 2012, 6:30-9:00 p.m.

3)      NIDA/INSERM Workshop on US-France Collaboration on Drug Abuse and Addiction Research – Monday, October, 15, 2012, 6:30-9:00 p.m.

4)      NIH Grant Workshop for Early Career Investigators – Tuesday, October 16, 2012, 6:30-9:00 p.m.

Information on these events can also be found at:

Top 25 Search Terms at NIF from June 11 to July 11

Posted on July 12th, 2012 in General information, Inside NIF, News & Events | No Comments »

Here are the top 25 search terms at NIF from June 11 to July 11:

1.            antibodyregistry

2.            database

3.            “Cingulate Cortex”

4.            “Purkinje Cell”

5.            “Hypothalamus”

6.            “Commissure of Fornix”

7.            cerebellum

8.            “Brainstem”

9.            “Forebrain”

10.          “Drug Related Gene Database”

11.          “Cerebellum”

12.          “Frontal Lobe”

13.          schizophrenia

14.          “Hair Cell”

15.          “Mitral Cell”

16.          “Oligodendrocyte Precursor Cell”

17.          glioma

18.          hippocampus

19.          receptive field

20.          “Amygdala”

21.          “Cerebral Crus”

22.          “Cone Cell”

23.          “Fornix”

24.          antibodyregistry gene:grm1

25.          “Anterior Nuclear Group”