jr trains in japan

just a few quick questions about trains and about this website: http://www.hyperdia.com/cgi-english/hyperWeb.cgi . Does this website only include JR trains in its database? or if it doesn't is there a way in which i can select criteria for it to only use JR trains?

Also, what is the limited express and nozomi? and are these trains, and the trains on the above website, valid to use with a Japan Rail Pass?

Does this website only include JR trains in its database?

No, it includes all trains in Japan, including non-JR trains.

is there a way in which i can select criteria for it to only use JR trains?

No.

Also, what is the limited express and nozomi? and are these trains, and the trains on the above website, valid to use with a Japan Rail Pass?

Limited express is a train category, which stops only at major stations. It is explained here:
http://www.japan-guide.com/e/e2016.html

JR limited express trains are covered by the Japan Rail Pass.

Nozomi is the fastest of three train categories on the JR Tokaido Shinkansen. It is one of the few JR trains, which are not covered by the Japan Rail Pass.

More details:
http://www.japan-guide.com/e/e2018.html
http://www.japan-guide.com/e/e2361.html

Hyperdia usually distinguishes non JR trains by naming the operating company.
I imagine you don't read Japanese but in case you do this map distinguishes JR from private rail. JR are the black and white alternating lines. Non JR are thin black. Thin black can also be monorails, people movers and tramways. Broken lines indicate below ground and subways.
http://www.mapion.co.jp/c/f?el=139/46/13.597&scl=10000&size=...

You might find this helpful:

http://www.japanrail.com/JR_hyperdia.html

Thanks for your replies. I read the website you suggested Steve, and it says this:

�gNEW! Hyperdia can now help you find trains you can use with a Japan Rail Pass. If you click the Except Nozomi button on the second page, where you insert your choice of times, you will get schedules only for Hikari and Kodama trains on the Tokaido/Sanyo Shinkansen lines. These are the trains that Japan Rail Pass holders must use when travelling between Tokyo and Kyoto, Osaka, Hiroshima and other points on these lines.�h

Does this mean that pressing this button will result in only JR trains, as JR trains are the only trains you can use with a Japan Rail Pass? For example, I searched from Tokyo to Fukuoka on December 9 10:00am, excepting the Nozomi. I think all Shinkansen are JR (aren�ft they?), and it says I will need to make two transfers: SHINKANSEN MAX TOKI 317 to LTD.EXP HAKUTAKA 8, and LTD.EXP HAKUTAKA 8 to JR Hokuriku Line. I�fm assuming that the Shinkansen is JR, and obviously the last train would be, but how do I know whether the LTD.EXP HAKUTAKA 8 is JR or not?

Thanks again! :))

ALL Shinkansen trains are JR.

By pressing "except Nozomi" doesn't necessarily weed out non JR trains, especially if you are doing non major city pairs.

For "Limited Express trains" if it has a picture like this:
http://grace.hyperdia.com/cgi-english/img/express.gif
Then its a JR train.

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HOWEVER
[BS]IF YOU WANT TO TRAVEL TO FUKUOKA[BE] the train station for Fukuoka is NOT FUKUOKA Station.

The main station for Fukuoka is HAKATA STATION.

"Fukuoka Station" is the name of some station in some place you'd probably not travel to in another direction.

I didn't notice but on that same page:
http://www.japanrail.com/JR_hyperdia.html

Its clearly said under "How to Enter Station names".

Another outstanding examples of Station names not being in the same place is "Shimoda Station" is not the station for if you want to travel to Shimoda. The train station for Shimoda is "Izukyu Shimoda".
Another recent example was Kawaguchi vs Kawaguchiko.

So BE CAREFUL in what you enter, research the Japan guide travel pages, to make sure you enter correct station names, or you'll end up no where close to where you want to be. For example if you went to Fukuoka Station, you'll be off course.

On Hyperdia this is how you tell its JR:

If it says: Shinkansen its JR. All Shinkansen trains are JR. It will also display a blue train picture/graphic.

If it BEGINS with LTD EXP. its JR. (it will also display a white train picture/graphic instead of a orange one, it will ONLY do this for JR limited express trains).

For local trains if it begins with JR its JR. Example
(JR xx line)

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How to tell its not JR:

It starts with the name of another railroad company ex: (Tokyo Metro XX Line) vs (JR XX Line). (Kintetsu xx line) (Osaka subway xx line) anything that has a name of a railroad preceding the name is not JR.

For Limited Express trains, non JR Limited Express trains will start with the name of the company followed by Ltd. Exp. but JR trains will always start with LTD EXP. and a picture/graphic of a white train vs a orange train.
On Hyperdia this is how you tell its JR:

If it says: Shinkansen its JR.

If it BEGINS with LTD EXP. its JR.

If it begins with JR its JR.

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How to tell its not JR:
It doesn't say Shinkansen.

It starts with the name of another railroad company ex: (Tokyo Metro Tozai Line).

For Limited Express trains, non JR Limited Express trains will start with the name of the company followed by Ltd. Exp. but JR trains will always start with LTD EXP. and a picture/graphic of a white train vs a orange train.

Thankyou everyone for your help, that has made it much clearer. Thanks again!!!!! :)))